Antibodies directed to the deletion mutants of epidermal growth factor receptor and uses thereof

ABSTRACT

The present invention relates to novel antibodies, particularly antibodies directed against deletion mutants of epidermal growth factor receptor and particularly to the type III deletion mutant, EGFRvIII. The invention also relates to human monoclonal antibodies directed against deletion mutants of epidermal growth factor receptor and particularly to EGFRvIII. Diagnostic and therapeutic formulations of such antibodies, and immunoconjugates thereof, are also provided.

RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application Ser.No. 60/562,453 filed Apr. 15, 2004, Ser. No. 60/525,570, filed Nov. 26,2003, and Ser. No. 60/483,145, filed Jun. 27, 2003, hereby incorporatedby reference in their entireties.

FIELD OF THE INVENTION

The present embodiments relate to novel antibodies, particularlyantibodies directed against deletion mutants of epidermal growth factorreceptor and particularly to the type III deletion mutant, EGFRvIII. Theembodiments also relate to human monoclonal antibodies directed againstdeletion mutants of epidermal growth factor receptor and particularly toEGFRvIII. The embodiments also relate to variants of such antibodies.Diagnostic and therapeutic formulations of such antibodies, andimmunoconjugates thereof, are also provided.

BACKGROUND OF THE INVENTION

Tumor specific molecules to aid in better diagnosis and treatment ofhuman and animal cancer have been sought since the last century. Hardevidence of tumor-specific substances, based on molecular structuraldata, has been difficult to provide in most types of human cancer exceptthose based on virally-induced cancer and involving molecular structuresspecified by the virus genome. There have been extremely few examples oftumor-specific molecules based on novel molecular structures. In thecase of malignant human gliomas and other tumors potentially associatedwith amplification or changes in the epidermal growth factor receptormolecule, such as carcinoma of the breast and other human carcinomas,there have been no unequivocal demonstrations of structurally alteredmolecules with unique sequences.

The epidermal growth factor receptor (EGFR) is the 170 kilodaltonmembrane glycoprotein product of the proto-oncogene c-erb B. Thesequence of the EGFR gene is known (Ullrich et al. (1984). HumanEpidermal Growth Factor Receptor cDNA Sequence and Aberrant Expressionof the Amplified Gene in A431 Epidermoid Carcinoma Cells. Nature309:418-425). The EGFR gene is the cellular homolog of the erb Boncogene originally identified in avian erythroblastosis viruses(Downward et al. (1984). Close Similarity of Epidermal Growth FactorReceptor and v-erb B Oncogene Protein Sequence. Nature 307:521-527,Ullrich, et al. (1984)). Activation of this oncogene by geneamplification has been observed in a variety of human tumors (Haley etal. (1987A). The Epidermal Growth Factor Receptor Gene in: Oncogenes,Genes, and Growth Factors Edited by: Guroff, G. 12th Edition. Chapter 2.pp. 40-76. Wiley, N.Y.), and in particular, those of glial origin(Libermann et al. (1985). Amplification, Enhanced Expression andPossible Rearrangement of EGF Receptor Gene in Primary Human BrainTumours of Glial Origin. Nature 313:144-147; Wong et al. (1987).Increased Expression of the Epidermal Growth Factor Receptor Gene inMalignant Gliomas is Invariably Associated with Gene Amplification.Proc. Natl. Acad. Sci. USA 84:6899-6903; Yamazaki et al. (1988).Amplification of the Structurally and Functionally Altered EpidermalGrowth Factor Receptor Gene (c-erbB) in Human Brain Tumors. Molecularand Cellular Biology 8:1816-1820; Malden et al., (1988). SelectiveAmplification of the Cytoplasmic Domain of the Epidermal Growth FactorReceptor Gene in Glioblastoma Multiforme. Cancer Research 4:2711-2714).

EGF-r has been demonstrated to be overexpressed on many types of humansolid tumors. Mendelsohn Cancer Cells 7:359 (1989), Mendelsohn CancerBiology 1:339-344 (1990), Modjtahedi and Dean Int'l J. Oncology4:277-296 (1994). For example, EGFR overexpression has been observed incertain lung, breast, colon, gastric, brain, bladder, head and neck,ovarian, kidney and prostate carcinomas. Modjtahedi and Dean Int'l J.Oncology 4:277-296 (1994). Both epidermal growth factor (EGF) andtransforming growth factor-alpha (TGF-alpha.) have been demonstrated tobind to EGF-r and to lead to cellular proliferation and tumor growth.

One major difference between v-erb B oncogenes and the normal EGFR geneis that the viral oncogenes are amino-truncated versions of the normalreceptor; they lack most of the extracytoplasmic domain but retain thetransmembrane and tyrosine kinase domains (Fung et al., (1984)Activation of the Cellular Oncogene c-erb B by LTR Insertion: MolecularBasis for Induction of Erythroblastosis by Avian Leukosis Virus. Cell33:357-368; Yamamoto et al., (1983). A New Avain Erythroblastosis Virus,AEV-H Carries erbB Gene Responsible for the Induction of BothErythroblastosis and Sarcoma. Cell 34:225-232, Nilsen et al., (1985).c-erbB Activation in ALV-Induced Erythroblastosis: Novel RNA Processingand Promoter Insertion Results in Expression of an Amino-Truncated EGFReceptor. Cell 41:719-726; Gammett et al., (1986). Differences inSequences Encoding the Carboxy-Terminal Domain of the Epidermal GrowthFactor Receptor Correlate with Differences in the Disease Potential ofViral erbB Genes. Proc. Natl. Acad. Sci. USA 83:6053-6057). This resultsin a protein that is unable to bind epidermal growth factor (EGF) butcan still phosphorylate other substrates (Gilmore et al., (1985).Protein Phosphorlytion at Tyrosine is Induced by the v-erb B GeneProduct in Vivo and In Vitro. Cell 40:609-618; Kris et al., (1985).Antibodies Against a Synthetic Peptide as a Probe for the KinaseActivity of the Avian EGF Receptor and v-erB Protein. Cell 40:619-625),and has led to speculation that the v-erb B proteins are oncogenicbecause the kinase domain is unregulated and constitutively active(Downward et al., 1984).

A variety of genetic alterations can occur in viral erb B oncogenes,e.g. amino acid substitutions and deletions in the carboxy terminus ofthe gene. Available evidence, however, argues that the amino truncationis critical to carcinogenesis. Amino truncations are a feature of allv-erb B oncogenes, including those that arise by promoter insertion orretroviral transduction (Nilsen et al., (1985). c-erbB Activation inALV-Induced Erythroblastosis: Novel RNA Processing and PromoterInsertion Results in Expression of an Amino-Truncated EGF Receptor. Cell41:719-726; Gammett et al., (1986). Differences in Sequences Encodingthe Carboxy-Terminal Domain of the Epidermal Growth Factor ReceptorCorrelate with Differences in the Disease Potential of Viral erbB Genes.Proc. Natl. Acad. Sci. USA 83:6053-6057).

In contrast, carboxy-terminal deletions appear to be associated onlywith tumors that arise through retroviral transduction and seem todetermine host range and tumor type specificity (Gammett et al., 1986;Raines et al., (1985). c-erbB Activation in Avian Leukosis Virus-InducedErythroblastosis: Clustered Integration Sites and the Arrangement ofProvirus in the c-erbB Alleles. Proc. Natl. Acad. Sci. USA82:2287-2291). Transfection experiments with amino-truncated avian c-erbB genes or chimeric viral oncogene-human EGF receptors demonstrates thatthis deletion is sufficient alone to create a transforming protein(Pelley et al., (1988). Proviral-Activated c-erbB is Leukemogenic butnot Sarcomagenic: Characterization of a Replication—Competent RetrovirusContaining the Activated c-erbB. Journal of Virology 62: 1840-1844;Wells et al., (1988). Genetic Determinants of Neoplastic Transformationby the Retroviral Oncogene v-erbB. Proc. Natl. Acad. Sci. USA85:7597-7601).

Amplification of the EGFR gene occurs in 40% of malignant human gliomas(Libermann et al., (1985) Amplification, Enhanced Expression andPossible Rearrangement of EGF Receptor Gene in Primary Human BrainTumours of Glial Origin. Nature 313:144-147; Wong et al., (1987).Increased Expression of the Epidermal Growth Factor Receptor Gene inMalignant Gliomas is Invariably Associated with Gene Amplification.Proc. Natl. Acad. Sci. USA 84:6899-6903), Rearrangement of the receptorgene is evident in many of the tumors with gene amplification. Thestructural alterations seem to preferentially affect the amino terminalhalf of the gene (Yamazaki et al., (1985). Amplification, EnhancedExpression and Possible Rearrangement of EGF Receptor Gene in PrimaryHuman Brain Tumours of Glial Origin. Nature 313:144-147; Malden et al.,(1988). Selective Amplification of the Cytoplasmic Domain of theEpidermal Growth Factor Receptor Gene in Glioblastoma Multiforme. CancerResearch 4:2711-2714), but the nature of the rearrangements had not atthat time been precisely characterized in any tumor.

Size variant EGFR genes and amplification have been reported in severalhuman cancers. (Humphrey et al., (1988). Amplification and Expression ofthe Epidermal Growth Factor Receptor Gene in Human Glioma Xenografts.Cancer Research 48:2231-2238; Bigner et al., (1988) J. Neuropathol. Exp.Neurol., 47:191-205; Wong et al., (1987). Increased Expression of theEpidermal Growth Factor Receptor Gene in Malignant Gliomas is InvariablyAssociated with Gene Amplification. Proc. Natl. Acad. Sci. USA84:6899-6903; and Humphrey et al. Amplification and expression of theepidermal growth factor receptor gene in human glioma xenografts. CancerRes. 48(8):2231-8 (1988)) There had been no determination, however, ofthe molecular basis for the altered EGFR molecules in cells.

In 1989, work of Drs. Bigner and Vogelstein elucidated the sequence of aEGF receptor mutant that has become known as the type III mutant (alsoreferred to as delta-EGFr or EGFrvIII). This work is described in U.S.Pat. Nos. 6,455,498, 6,127,126, 5,981,725, 5,814,317, 5,710,010,5,401,828, and 5,212,290, the disclosures of which are herebyincorporated by reference.

EGFR variants are caused by gene rearrangement accompanied by EGFR geneamplification. There are eight major variants of EGFr that are known:(i) EGFRvI lacks a majority of the extracellular domain of EGFR, (ii)EGFRvII consists of an 83 aa in-frame deletion in the extracellulardomain of EGFR, (iii) EGFRvIII consists of a 267 aa in-frame deletion inthe extracellular domain of EGFR, (iv) EGFRvIV contains deletions in thecytoplasmic domain of EGFR, (v) EGFRvV contains deletions in cytoplasmicdomain of EGFR, (vi) EGFR.TDM/2-7 contains a duplication of exons 2-7 inthe extracellular domain of EGFR, (vii) EGFR.TDM/18-25 contains aduplication of exons 18-26 in the tyrosine kinase domain of EGFR, and(viii) EGFR.TDM/18-26 contains a duplication of exons 18-26 in thetyrosine kinase domain of EGFR (Kuan et al. EGF mutant receptor vIII asa molecular target in cancer therapy. Endocr Relat Cancer. 8(2):83-96(2001)). In addition, there is a second, more rare, EGFRvIII mutant(EGFRvIII/Al2-13) that possesses a second deletion that introduces anovel histidine residue at the junction of exons 11 and 14 (Kuan et al.EGF mutant receptor vIII as a molecular target in cancer therapy. EndocrRelat Cancer. 8(2):83-96 (2001)).

EGFRvIII is the most commonly occurring variant of the epidermal growthfactor (EGF) receptor in human cancers (Kuan et al. EGF mutant receptorvIII as a molecular target in cancer therapy. Endocr Relat Cancer.8(2):83-96 (2001)). During the process of gene amplification, a 267amino acid deletion occurs in the extracellular domain creating a noveljunction to which tumor specific monoclonal antibodies can be directed.This variant of the EGF receptor contributes to tumor progressionthrough constitutive signaling in a ligand independent manner. EGFrVIIIis not know to be expressed on any normal tissues (Wikstrand, C J. etal. Monoclonal antibodies against EGFR_(v)III are tumor specific andreact with breast and lung carcinomas malignant gliomas. Cancer Research55(14): 3140-3148 (1995); Olapade-Olaopa, E O. et al. Evidence for thedifferential expression of a variant EGF receptor protein in humanprostate cancer. Br J Cancer. 82(1):186-94 (2000)). Yet, EGFRvIII showssignificant expression in tumor cells, e.g., 27˜76% breast cancerbiopsies express EGFRvIII (Wikstrand, C J. et al. Monoclonal antibodiesagainst EGFR_(v)III are tumor specific and react with breast and lungcarcinomas malignant gliomas. Cancer Research 55(14): 3140-3148 (1995);Ge H. et al. Evidence of high incidence of EGFRvIII expression andcoexpression with EGFR in human invasive breast cancer by laser capturemicrodissection and immunohistochemical analysis. Int J Cancer.98(3):357-61 (2002)), 50-70% gliomas express EGFRvIII (Wikstrand, C J.et al. Monoclonal antibodies against EGFR_(v)III are tumor specific andreact with breast and lung carcinomas malignant gliomas. Cancer Research55(14): 3140-3148 (1995); Moscatello, G. et al. Frequent expression of amutant epidermal growth factor receptor in multiple human tumors. CancerRes. 55(23):5536-9 (1995)), 16% NSCL cancers express EGFRvIII (Garcia dePalazzo, I E. et al. Expression of mutated epidermal growth factorreceptor by non-small cell lung carcinomas. Cancer Res. 53(14):3217-20(1993)), 75% ovarian cancers express EGFRvIII (Moscatello, G. et al.Frequent expression of a mutant epidermal growth factor receptor inmultiple human tumors. Cancer Res. 55(23):5536-9 (1995)), and 68%prostate cancers express EGFRvIII (Olapade-Olaopa, E O. et al. Evidencefor the differential expression of a variant EGF receptor protein inhuman prostate cancer. Br J Cancer. 82(1):186-94 (2000)).

The deletion of 267 amino acids with a Glycine substitution creates aunique junction that may be capable of antibody targeting. Further, inview of EGFRvIII's expression in certain tumors and its lack ofexpression in normal tissues, EGFRvIII may be an ideal target for drugtargeting in tumor therapy. In particular, EGFRvIII would appear to bean ideal candidate for immunoconjugate therapy of tumors (e.g., anantibody conjugated to an antineoplastic agent or toxin). Another methodof treatment of cancers which over-express EGFRvIII involved the use ofa tumor-specific ribozyme targeted specifically to the variant receptorwhich did not cleave normal EGFR. The ribozyme was found tosignificantly inhibit breast cancer growth in athymic nude mice (Luo etal. Int. J. Cancer. 104(6):716-21 (2003)).

General antibodies for the entire EGFRvIII protein have been described.See International Patent Application No. WO 01/62931 and Kuan et al. EGFmutant receptor vIII as a molecular target in cancer therapy. EndocrRelat Cancer. 8(2):83-96 (2001), Kuan et al. EGFRvIII as a promisingtarget for antibody-based brain tumor therapy. Brain Tumor Pathol.17(2):71-78 (2000), Kuan et al. Increased binding affinity enhancestargeting of glioma xenografts by EGFRvIII-specific scFv. InternationalJournal of Cancer. 88(6):962-969 (2000), Landry et al. Antibodyrecognition of a conformational epitope in a peptide antigen: Fv-peptidecomplex of an antibody fragment specific for the mutant EGF receptor,EGFRvIII. Journal of Molecular Biology. 308(5):883-893 (2001), Reist etal. Astatine-211 labeling of internalizing anti-EGFRvIII monoclonalantibody using N-succinimidyl 5-[211At]astato-3-pyridinecarboxylate.Nuclear Medicine and Biology. 26(4):405-411 (1999), Reist et al. Invitro and in vivo behavior of radiolabeled chimeric anti-EGFRvIIImonoclonal antibody: comparison with its murine parent. Nuclear Medicineand Biology. 24(7):639-647 (1997), Wikstrand et al. Generation ofanti-idiotypic reagents in the EGFRvIII tumor-associated antigen system.Cancer Immunology, Immunotherapy. 50(12):639-652 (2002), Wikstrand etal. Monoclonal antibodies against EGFRvIII are tumor specific and reactwith breast and lung carcinomas malignant gliomas. Cancer Research.55(14):3140-3148 (1995), Wikstrand et al. The class III variant of theepidermal growth factor receptor (EGFR_(v)III): characterization andutilization as an immunotherapeutic target. J. Neurovirol. 4(2):148-158(1998), Wikstrand et al. The class III variant of the epidermal growthfactor receptor (EGFRvIII): characterization and utilization as animmunotherapeutic target. J. Neurovirol. 4(2):148-158 (1998), Jungbluthet al. A monoclonal antibody recognizing human cancers withamplification/overexpression of the human epidermal growth factorreceptor. Proc Natl Acad Sci U S A. 100(2):639-44 (2003), Mamot et al.Epidermal Growth Factor Receptor (EGFR)-targeted Immunoliposomes MediateSpecific and Efficient Drug Delivery to EGFR- andEGFRvIII-overexpressing Tumor Cells. Cancer Research 63:3154-3161(2003)). Each of these above-mentioned antibodies, however, possess orcontain murine sequences in either the variable and/or constant regions.The presence of such murine derived proteins can lead to the rapidclearance of the antibodies or can lead to the generation of an immuneresponse against the antibody in a patient. In addition, such antibodiesare relatively low affinity, on the order of 2.2×10⁻⁸ through 1.5×10⁻⁹,even after affinity maturation. (Kuan et al. EGF mutant receptor vIII asa molecular target in cancer therapy. Endocr Relat Cancer. 8(2):83-96(2001)).

In order to avoid the utilization of murine or rat derived antibodies,researchers have introduced human antibody function into rodents so thatthe rodents can produce fully human antibodies. See e.g., Mendez et al.Functional transplant of megabase human immunoglobulin locirecapitulates human antibody response in mice. Nat Genet. 15(2):146-56(1997). This approach has been used in connection with the generation ofsuccessful antibodies directed against wild type EGFR. See e.g., Yang Xet al. Development of ABX-EGF, a fully human anti-EGF receptormonoclonal antibody, for cancer therapy. Crit Rev Oncol Hemato38(1):17-23 (2001); Yang X-D et al. Eradication of Established Tumors bya Fully Human Monoclonal Antibody to the Epidermal Growth FactorReceptor without Concomitant Chemotherapy. Cancer Research59(6):1236-1243 (1999); and U.S. Pat. No. 6,235,883.

SUMMARY OF THE INVENTION

In one embodiment, the invention comprises an isolated human monoclonalantibody that specifically binds to EGFRvIII and a peptide thatcomprises the sequence L E E K K G N Y V V T D H C (SEQ ID NO: 56). Inone embodiment, a therapeutic agent may be conjugated to the antibody.In one embodiment, a toxin is used. In another embodiment, the inventioncomprises an isolated human monoclonal antibody that specifically bindsto an epitope contained within a sequence comprising L E E K K G N Y V VT D H C (SEQ ID NO: 56), wherein the residues required for binding, asdetermined by Alanine scanning in a SPOTs array, are selected from thegroup consisting of EEK, KKNYV, LEK, EKNY and EEKGN.

Further embodiments include an isolated human monoclonal antibody thatcomprises a heavy chain variable region amino sequence that is encodedby a VH3-33 gene. The heavy chain variable region amino sequence caninclude an amino acid sequence that is encoded by a JH4b gene, or anamino acid sequence that is encoded by a D gene that is selected fromthe group consisting of D6-13 and D3-9.

Other embodiments include an isolated human monoclonal antibody thatcomprises a light chain variable region amino sequence that is encodedby a A23(VK2) gene. The light chain variable region amino sequence caninclude an amino acid sequence that is encoded by a JK1 gene.

Other embodiments include an isolated antibody, or fragment thereof,that binds to EGFRvIII and that comprises a heavy chain amino acidsequence selected from the group consisting of the heavy chain aminoacid sequence of antibody 13.1.2, 131, 170, 150, 095, 250, 139, 211,124, 318, 342 and 333 as identified in (SEQ ID NO: 138, 2, 4, 5, 7, 9,10, 12, 13, 15, 16, and 17). The antibody can be a monoclonal antibody,a chimeric antibody, a humanized antibody or a human antibody. Theantibody or fragment can be associated with a pharmaceuticallyacceptable carrier or diluent, and can be conjugated to a therapeuticagent. The therapeutic agent can be a toxin. The therapeutic agent canbe a toxin such as DM-1, AEFP, AURISTATIN E, or ZAP. The agent can beassociated with the antibody via a linker. The toxin can be associatedwith the antibody via a secondary antibody. Further embodiments includea hybridoma cell line producing the antibody, and a transformed cellcomprising a gene encoding the antibody. The cell can be, for example, aChinese hamster ovary cell.

Further embodiments include a method of, inhibiting cell proliferationassociated with the expression of EGFRvIII, comprising treating cellsexpressing EGFRvIII with an effective amount of the antibody orfragment. In one emobidment, the antibody comprises a heavy chain aminoacid sequence selected from the group consisting of the heavy chainamino acid sequence of antibody 13.1.2 (SEQ ID NO: 138), 131 (SEQ ID NO:2), 170 (SEQ ID NO: 4), 150 (SEQ ID NO: 5), 095 (SEQ ID NO: 7), 250 (SEQID NO: 9), 139 (SEQ ID NO: 10), 211 (SEQ ID NO: 12), 124 (SEQ ID NO:13), 318 (SEQ ID NO: 15), 342 (SEQ ID NO: 16), and 333 (SEQ ID NO: 17).The method can be performed in vivo, and performed on a mammal, such asa human, who suffers from a cancer involving epithelial cellproliferation, such as a lung, colon, gastric, renal, prostate, breast,glioblastoma or ovarian carcinoma.

Further embodiments include a method of killing a targeted cell. This isachieved by contacting the targeted cell with an antibody associatedwith a toxin. The antibody binds to a peptide LEEKKGNY (SEQ ID NO: 133).In one embodiment, the antibody has a binding affinity greater than1.3*10⁻⁹M to the peptide. In one embodiment the toxin is selected fromAEFP, MMAE, DM-1, and ZAP. In one embodiment, the antibody toxincompound is 10 fold more toxic to targeted cells than to cells withoutthe peptide. In one embodiment, the antibody comprises a heavy chainamino acid sequence selected from the group consisting of the heavychain amino acid sequence of antibody 13.1.2 (SEQ ID NO: 138), 131 (SEQID NO: 2), 170 (SEQ ID NO: 4), 150 (SEQ ID NO: 5), 095 (SEQ ID NO: 7),250 (SEQ ID NO: 9), 139 (SEQ ID NO: 10), 211 (SEQ ID NO: 12), 124 (SEQID NO: 13), 318 (SEQ ID NO: 15), 342 (SEQ ID NO: 16), and 333 (SEQ IDNO: 17). In another embodiment, the antibody is associated with a toxinvia a peptide linker or a second antibody.

Further embodiments of the invention include an isolated antibody thatbinds to EGFRvIII and that comprises a heavy chain amino acid sequencecomprising the following complementarity determining regions (CDRs):

-   -   (a) CDR1 consisting of a sequence selected from the group        consisting of the amino acid sequences for the CDR1 region of        antibodies 13.1.2, 131, 170, 150, 095, 250, 139, 211, 124, 318,        342 and 333 as identified in SEQ ID NO: 138, 2, 4, 5, 7, 9, 10,        12, 13, 15, 16, and 17;    -   (b) CDR2 consisting of a sequence selected from the group        consisting of the amino acid sequences for the CDR2 region of        antibodies 13.1.2, 131, 170, 150, 095, 250, 139, 211, 124, 318,        342 and 333 as identified in SEQ ID NO: 138, 2, 4, 5, 7, 9, 10,        12, 13, 15, 16, and 17; and    -   (c) CDR3 consisting of a sequence selected from the group        consisting of the amino acid sequences for the CDR3 region of        antibodies 13.1.2, 131, 170, 150, 095, 250, 139, 211, 124, 318,        342 and 333 as identified in SEQ ID NO: 138, 2, 4, 5, 7, 9, 10,        12, 13, 15, 16, and 17. In one embodiment, the antibody is a        monoclonal antibody, a chimeric antibody, human, or a humanized        antibody. In one embodiment, the antibody is associated with a        pharmaceutically acceptable carrier, diluent, and/or therapeutic        agent. In one embodiment, the therapeutic agent is a toxin. In        one embodiment, the toxin is DM-1 or Auristatin E.

Also included is an isolated antibody, or fragment thereof, that bindsto EGFRvIII and that comprises a light chain amino acid sequenceselected from the group consisting of the light chain amino acidsequence of antibody 13.1.2, 131, 170, 150, 123, 095, 139, 250, 211,318, 342, and 333 as identified in SEQ ID NO: 140, 19, 20, 21, 29, 23,25, 26, 28, 33, 31 and 32. The antibody can be a monoclonal antibody, achimeric antibody, a humanized antibody, or a human antibody. It can beassociated with a pharmaceutically acceptable carrier or diluent, orconjugated to a therapeutic agent, such as a toxin, for example DM1 orAURISTATIN E. In one embodiment a hybridoma cell line or a transformedcell producing an antibody comprising a light chain amino acid sequenceselected from the group consisting of the light chain amino acidsequence of antibody 13.1.2, 131, 170, 150, 123, 095, 139, 250, 211,318, 342, and 333 as identified in SEQ ID NO: 140, 19, 20, 21, 29, 23,25, 26, 28, 33, 31 and 32 is contemplated.

Further embodiments include a hybridoma cell line producing such anantibody, and a transformed cell, such as a Chinese hamster ovary cell,comprising a gene encoding the antibody.

Yet another embodiment includes a method of inhibiting cellproliferation associated with the expression of EGFRvIII, comprisingtreating cells expressing EGFRvIII with an effective amount of theantibodies or fragments described above. The method can be performed invivo and on a mammal, such as a human, who suffers from a cancerinvolving epithelial cell proliferation such as lung, colon, gastric,renal, prostate, breast, glioblastoma or ovarian carcinoma.

Yet another embodiment includes an isolated antibody that binds toEGFRvIII and that comprises a light chain amino acid sequence comprisingthe following complementarity determining regions (CDRs):

-   -   (a) CDR1 consisting of a sequence selected from the group        consisting of the amino acid sequences for the CDR1 region of        antibodies 13.1.2, 131, 170, 150, 123, 095, 139, 250, 211, 318,        342, and 333 as identified in SEQ ID NO: 140, 19, 20, 21, 29,        23, 25, 26, 28, 33, 31 and 32;    -   (b) CDR2 consisting of a sequence selected from the group        consisting of amino acid sequences for the CDR1 region of        antibodies 13.1.2, 131, 170, 150, 123, 095, 139, 250, 211, 318,        342, and 333 as identified in SEQ ID NO: 140, 19, 20, 21, 29,        23, 25, 26, 28, 33, 31 and 32; and    -   (c) CDR3 consisting of a sequence selected from the group        consisting of amino acid sequences for the CDR1 region of        antibodies 13.1.2, 131, 170, 150, 123, 095, 139, 250, 211, 318,        342, and 333 as identified in SEQ ID NO: 140, 19, 20, 21, 29,        23, 25, 26, 28, 33, 31 and 32.

The antibody described in the paragraph above can also include a heavychain amino acid sequence comprising the following complementaritydetermining regions (CDRs):

-   -   (a) CDR1 consisting of a sequence selected from the group        consisting of the amino acid sequences for the CDR1 region of        antibodies 13.1.2, 131, 170, 150, 095, 250, 139, 211, 124, 318,        342 and 333 as identified in SEQ ID NO: 138, 2, 4, 5, 7, 9, 10,        12, 13, 15, 16, and 17;    -   (b) CDR2 consisting of a sequence selected from the group        consisting of the amino acid sequences for the CDR2 region of        antibodies 13.1.2, 131, 170, 150, 095, 250, 139, 211, 124, 318,        342 and 333 as identified in SEQ ID NO: 138, 2, 4, 5, 7, 9, 10,        12, 13, 15, 16, and 17; and    -   (c) CDR3 consisting of a sequence selected from the group        consisting of the amino acid sequences for the CDR3 region of        antibodies 13.1.2, 131, 170, 150, 095, 250, 139, 211, 124, 318,        342 and 333 as identified in SEQ ID NO: 138, 2, 4, 5, 7, 9, 10,        12, 13, 15, 16, and 17.

Further embodiments include a method of inhibiting cell proliferationassociated with the expression of EGFRvIII, comprising treating cellsexpressing EGFRvIII with an effective amount of the antibody or fragmentdescribed above. The method can be performed in vivo, on a mammal, suchas a human, suffering from a cancer involving epithelial cellproliferation, such as lung carcinoma, breast carcinoma, head & neckcancer, prostate carcinoma or glioblastoma.

Further embodiments include an isolated polynucleotide moleculecomprising a nucleotide sequence encoding a heavy chain amino acidsequence, or a fragment thereof, selected from the group consisting ofthe heavy chain amino acid sequence of antibodies 13.1.2, 131, 170, 150,095, 250, 139, 211, 124, 318, 342, and 333 as identified in SEQ ID NO:138, 2, 4, 5, 7, 9, 10, 12, 13, 15, 16, and 17, or an isolatedpolynucleotide molecule comprising a nucleotide sequence encoding alight chain amino acid sequence, or a fragment thereof, selected fromthe group consisting of the light chain amino acid sequence ofantibodies 13.1.2, 131, 170, 150, 123, 095, 139, 250, 211, 318, 342, and333, as identified in SEQ ID NO: 140, 19, 20, 21, 29, 23, 25, 26, 28,33, 31 and 32.

Further embodiments include an article of manufacture comprising acontainer, a composition contained therein, and a package insert orlabel indicating that the composition can be used to treat cancercharacterized by the expression of EGFRvIII, wherein the compositioncomprises an antibody as described above. Such cancers include a lungcarcinoma, breast carcinoma, head & neck cancer, prostate carcinoma orglioblastoma. Also included is an assay kit for the detection ofEGFRvIII in mammalian tissues or cells in order to screen for lung,colon, gastric, renal, prostate or ovarian carcinomas, the EGFRvIIIbeing an antigen expressed by epithelial cancers, the kit comprising anantibody that binds the antigen protein and means for indicating thereaction of the antibody with the antigen, if present. The antibody canbe a labeled monoclonal antibody, or the antibody can be an unlabeledfirst antibody and the means for indicating the reaction comprises alabeled second antibody that is anti-immunoglobulin. The antibody thatbinds the antigen can be labeled with a marker selected from the groupconsisting of a fluorochrome, an enzyme, a Radionuclide and a radiopaquematerial. The antibody that binds the antigen can also bind toover-expressed wtEGFR. The kit can be used clinically for patientselection.

A further embodiment includes an antibody which specifically recognizesthe epitope of EGFRvIII containing the novel Gly residue.

A further embodiment includes a protein variant of EGFRvIII. The variantmay have a pFLAG insert, may consist of the amino acids in SEQ ID NO:56, and can exist in silico.

Another embodiment includes an antibody, or variant thereof, which bindsto the recognition sequence EEKKGNYVVT (SEQ ID NO: 57).

Another embodiment includes an antibody variant that specifically bindsto EGFRvIII. The antibody variant can further bind to a peptide thatcomprises SEQ ID NO: 57. The antibody variant can have residues thatinteract with residues EKNY or EEKGN in the peptide. In one embodiment,the antibody variant binds to the peptide sequence ten fold more tightlythan it does to a wild-type EGFR protein. In one embodiment, theantibody binds specifically binds to EGFRvIII and the peptide of SEQ IDNO: 56. In one embodiment, the isolated antibody or variant has acomplementarity determining region comprising a deep cavity, wherein thecavity is created by CDR2 and CDR3 of the heavy chain, CDR3 of the lightchain, and a small portion from CDR1 of the, light chain. In oneembodiment, the isolated antibody or variant has residues 31, 37,95-101, 143-147, 159, 162-166, 169-171, 211-219, 221, and 223 within 5angstroms of a binding cavity. In one embodiment, the isolated antibodyor variant has a complementarity determining region comprising a narrowgroove, wherein the groove is created by heavy chain CDR2 and CDR3, andlight chain CDR1, CDR2, and CDR3. In one embodiment, the isolatedantibody or variant has residues 31, 33, 35-39, 51, 54-56, 58-61,94-101, 144-148, 160, 163-166, 172, and 211-221 within 5 angstroms of abinding groove. In one embodiment, the isolated antibody or variant hasresidues 31-33, 35, 37, 55, 96-101, 148, 163, 165, 170, 172, 178, 217,and 218 within 5 angstroms of a binding groove. In one embodiment, theisolated antibody or variant has a paratope configured so that when theepitope of peptide EEKKGN (SEQ ID NO 127) binds to the paratope of theantibody, at least one bond is formed between two residues selected fromthe group consisting of E2 and Y172, K3 and H31, K4 and H31, N6 and D33,N6 and Y37, and N6 and K55. In one embodiment, the isolated antibody orvariant has a paratope configured so that when the epitope of peptideEEKKGNY (SEQ ID 131) binds to the paratope of the antibody, at least onebond is formed between two residues selected from the group consistingof K4 and Q95, K4 and Q95, N6 and Q98, G5 and H31, Y7 and H31, Y7 andW165. In one embodiment, the antibody has a structure or interactionwith a structure that is determined in silico.

Another embodiment provides a method for selecting variants that bind toEGFRvIII with particular binding characteristics, the method comprisingthe use of a molecular structure to create a paratope, the use of amolecular structure to create an epitope, calculating the interactionenergy between the two and comparing that energy level to the energylevel of the epitope and a second paratope of a mAb variant, andselecting a variant based on the differences in the energy levels. Themethod can further include using an interaction energy between a secondvariant of the paratope and the epitope to determine a third interactionenergy and comparing the third interaction energy and the secondinteraction energy to determine which variant to select. In oneembodiment, the variant is created and tested for binding.

Another embodiment provides a method for selecting variants that bind toEGFRvIII with particular binding characteristics, the method comprisingexamining residues of an epitope which interact with a paratope,selecting important residues to create a recognition sequence, usingthis sequence to create a EGFRvIII variant, and using the EGFRvIIIvariant to select the mAb variant.

Another embodiment provides a method for making antibody variants toEGFRvIII, said method comprising analyzing the residues of an epitopewhich interact with a paratope, selecting the more important residues ofan epitope to create a recognition sequence, using the recognitionsequence to create an EGFRvIII variant, and using the EGFRvIII variantto select antibody variants. In one embodiment, the selection of theantibodies is achieved in silico. In one embodiment, the selection ofthe antibodies through the use of the EGFRvIII variant is achieved byraising antibodies against EGFRvIII variant.

In the embodiment where the isolated antibody variant binds to EGFRvIIIand the peptide of SEQ ID NO: 57, the antibody can further comprise apoint mutation of the following: Tyr172Arg, Leu99Glu, Arg101Glu,Leu217Glu, Leu99Asn, Leu99His, L99T, Arg101Asp, or some combinationthereof. In one embodiment, the antibody is a monoclonal antibody, achimeric antibody, a humanized antibody, or a human antibody.

In one embodiment, the antibody or variant thereof binds to the sequenceEEKKGNYVVT (SEQ ID NO: 57), and the antibody or variant has subnanomolarbinding ability.

In a further embodiment, the antibody binds to EGFRvIII and the antibodyhas a paratope that binds to an epitope, and the epitope has a set ofresidues that interact with the paratope that include E, K, N, and Y. Inone embodiment, the antibody is antibody 131.

In a further embodiment, the antibody binds to EGFRvIII and the antibodyhas a paratope that binds to an epitope that has a set of residues thatinteract with the paratope Comprising: E, E, K, G, and N. In oneembodiment, the primary structure of the epitope is EEKKGNY (SEQ ID NO:131). In one embodiment, the antibody is 13.1.2.

In a further embodiment, the antibody that binds to EGFRvIII and has aK_(D) of less than 1.3*10⁻⁹ M, less than 1.0*10⁻⁹ M, or less than 500pM. In one embodiment, the antibody is specific for SEQ ID NO: 56compared to a wild type EGFR peptide. In one embodiment, the nonspecificbinding of the antibody to the wild type EGFR peptide (SEQ ID NO: 134)is less than 10% of that of the specific binding of the antibody toEGFRVIII (SEQ ID NO: 135). In one embodiment, the antibody is selectedfrom the group consisting of 131, 139, and 13.1.2. In one embodiment,the antibody is internalized. In one embodiment, the internalizationoccurs for at least about 70% or at least about 80% of the antibody.

In one embodiment, the variant human monoclonal antibody preferentiallybinds to an epitope that is substantially unique to an EGFRvIII proteincompared to a wild-type EGFR protein or variant thereof (SEQ ID NO:134). In one embodiment, the variant comprises a heavy chaincomplementarity determining region (CDR1) corresponding to canonicalclass 1. In one embodiment, the variant comprises a heavy chaincomplementarity determining region (CDR2) corresponding to canonicalclass 3. In one embodiment, the variant comprises a light chaincomplementarity determining region (CDR1) corresponding to canonicalclass 4. In one embodiment, the variant comprises a light chaincomplementarity determining region (CDR2) corresponding to canonicalclass 1. In one embodiment, the variant comprises a light chaincomplementarity determining region (CDR3) corresponding to canonicalclass 1. In one embodiment, the variant comprises a first heavy chaincomplementarity determining region (CDR1) corresponding to canonicalclass 1, a second heavy chain complementarity determining region (CDR2)corresponding to canonical class 3, a first light chain complementaritydetermining region (CDR1) corresponding to canonical class 4, a secondlight chain complementarity determining region (CDR2) corresponding tocanonical class 1; and a third light chain complementarity determiningregion (CDR3) corresponding to canonical class 1, wherein thecomplementary determining regions are configured to allow the variant tobind to an epitope that is substantially unique to an EGFRvIII proteinas compared to a EGFR protein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is an alignment between wild type EGFR and EGFRvIII showing the267 amino acid deletion and G substitution.

FIG. 2 is a diagram of the design of the EGFRvIII PEP3 14-mer peptide.In FIG. 2A, the N-terminal sequence of EGFRvIII with amino acids LEEKK(SEQ ID NO: 58) (1-5) that are identical to the N-terminal sequence ofEGFR, followed by the unique Glysine residue, followed by amino acidsthat are identical to residues 273 through 280 in EGFR. FIG. 2Brepresents the amino acids of EGFR that are deleted in EGFRvIII (6-272).

FIGS. 3A-L provide sequences of antibodies of the invention. For eachantibody provided, a nucleotide and amino acid sequence is provided forboth a heavy chain and a light chain variable region. Accordingly, foursequences are provided for every antibody listed.

FIG. 4 is a table comparing the 13.1.2 antibody heavy chain regions to aparticular germ line heavy chain region. “-”s indicate that the aminoacid residue of the hybridoma heavy chain region is the same as the germline for that particular position. Deviation from the germline isindicated by the appropriate amino acid residue.

FIG. 5 is a table comparing the 13.1.2 antibody light chain regions to aparticular germ line light chain region. “-”s indicate that the aminoacid residue of the hybridoma light chain region is the same as the germline for that particular position. Deviation from the germline isindicated by the appropriate amino acid residue.

FIG. 6 is a table comparing various hybridoma derived antibody heavychain regions to a particular germ line heavy chain region. “-”sindicate that the amino acid residue of the hybridoma heavy chain regionis the same as the germ line for that particular position. Deviationfrom the germline is indicated by the appropriate amino acid residue.

FIG. 7 is a table comparing various hybridoma derived antibody lightchain regions to a particular germ line light chain region. “-”sindicate that the amino acid residue of the hybridoma light chain regionis the same as the germ line for that particular position. Deviationfrom the germline is indicated by the appropriate amino acid residue.

FIG. 8 is a representative figure showing binding of recombinantEGFRvIII mAbs to cells expressing EGFRvIII (NR6 cells). Diamondsrepresent 95, triangles represent 133, squares represent 139, “x”represent 150, asterixes represent 170, circles represent 221, lines230, and rectangles represent 250.

FIG. 9A shows FACS staining analysis for a human anti-EGFR antibody(ABX-EGF) to H80.

FIG. 9B shows FACS staining analysis for antibody 131 to H80.

FIG. 9C shows FACS staining analysis for antibody 139 to H80.

FIG. 9D shows FACS staining analysis for antibody 13.1.2 to H80.

FIG. 9E shows FACS staining analysis for ABX-EGF to H1477.

FIG. 9F shows FACS staining analysis for antibody 131 to H1477.

FIG. 9G shows FACS staining analysis for antibody 139 to H1477.

FIG. 9H shows FACS staining analysis for antibody 13.1.2 to H1477.

FIG. 9I shows FACS staining analysis for ABX-EGF to A549.

FIG. 9J shows FACS staining analysis for antibody 131 to A549.

FIG. 9K shows FACS staining analysis for antibody 139 to A549.

FIG. 9L shows FACS staining analysis for antibody 13.1.2 to A549.

FIG. 9M is a graph displaying binding of EGFRvIII mAbs to glioblastomacells. Filled triangles represent antibody 131 binding to H1477. Filledsquares represent antibody 13.1.2 binding to H1477. Empty trianglesrepresent antibody 131 binding to H80. Empty squares represent antibody13.1.2 binding to H80.

FIG. 9N is a graph displaying the binding of EGFRvIII mAbs to humanepidermoid carcinoma cell line A431. The filled squares representantibody 13.1.2. The filled triangles represent antibody 131.

FIG. 9O is a graph displaying the binding of antibody 13.1.2 to NR6murine fibroblast cell lines. The squares represent NR6. The trianglesrepresent NR6 with with wild type EDFR. The circles represent NR6 withEGFRvIII.

FIG. 9P is a graph displaying the binding of antibody 131 to murinefibroblast cell lines. The squares represent NR6. The trianglesrepresent NR6 with wild type EGFR. The circles represent NR6 withEGFRvIII.

FIG. 10A shows FACS staining analysis for a human anti-EGFR antibody(ABX-EGF) binding to cells expressing EGFR (A431).

FIG. 10B shows FACS staining analysis for antibody 131 to cellsexpressing EGFR (A431).

FIG. 10C shows FACS staining analysis for antibody 139 to cellsexpressing EGFR (A431).

FIG. 10D shows FACS staining analysis for antibody 13.1.2 to cellsexpressing EGFR (A431).

FIG. 11 shows the molecular surface of antibody 131 structure model. Thesix CDRs are shaded different shades to mark their boundries. Thebinding cavity is located close to the center.

FIG. 12 shows a structural model of the molecular surface of antibody13.1.2. The six CDR regions are shaded and identified by number. Thelong groove is located approximately along the vertical centerline.

FIG. 13A is a possible docking model of the 13.1.2 antibody and peptideEEKKGN (SEQ ID NO: 127) complex. The CDR regions are shaded to denoteboundries.

FIG. 13B shows the hydrogen bonds in the docking model of the 13.1.2antibody and peptide EEKKGN (SEQ ID NO: 127) complex. Shading of the CDRloops and residues is the same as in FIG. 12. The peptide residue isnumbered from the N-terminus, at the top of the figure, to theC-terminus as 1 through 6. Six hydrogen bonds are indicated by dashedlines. The six pairs of amino acids forming hydrogen bonds are: E2 . . .Y172, K3 . . . H31, K4 . . . H31, N6 . . . D33, N6 . . . Y37, and N6 . .. K55.

FIG. 14 is a graph demonstrating a correlation between theepitope-antibody binding energy and the logarithm of Kd for one of thedocking models selected.

FIG. 15 is a depiction of a refined docking model for the peptide-13.1.2antibody complex. The peptide is rendered in a space-filling manner.

FIG. 16 is a depiction representing the hydrogen bonds in the refineddocking model.

FIG. 17 is a graph that depicts the linear fitting of antibody-antigenbinding energy versus the logarithm of relative affinities.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

As discussed above, EGFRvIII is a deletion mutant of EGFR in which 267amino acids in the extracellular domain of EGFr are deleted with asingle amino acid substitution of Glycine at the junction. Thesefeatures are shown in a sequence alignment between wild type EGFR andEGFRvIII in FIG. 1. In view of the amino acid substitution of Glycine atthe junction of the deletion, it becomes theoretically possible togenerate antibodies to the novel epitope present in EGFRvIII that is notpresent in wild type EGFR. Thus, a peptide for immunization andscreening was designed, termed PEP3, as shown in FIG. 2 (Kuan et al. EGFmutant receptor vIII as a molecular target in cancer therapy. EndocrRelat Cancer. 8(2):83-96 (2001)). Such 14-mer peptide possesses the 5n-terminal amino acids common to EGFRvIII and wild type EGFR, the uniqueGlycine junction site, and 8 amino acid residues contained in theconserved sequences between wild type EGFR (corresponding to residues273-280) and EGFRvIII (corresponding to residues 7-14). In addition,glioblastoma cell and cells (B300.19 cells) transfected with the geneencoding EGFRvIII were also utilized for immunization and screening(sometimes referred to herein as B300.19/EGFRvIII transfectants).

In order to generate human antibodies against EGFRvIII, transgenicXenoMouse® mice were immunized with combinations of glioblastomacells/EGFRvIII, B300.19/EGFRvIII cells, and peptides (PEP3) directed tothe junction region in the novel extracellular domain represented inEGFRvIII as compared to wild type EGFR. B cells from immunized mice wereisolated and either used to produce hybridomas followed by screening forbinding to EGFRvIII or used directly in screening for binding toEGFRvIII using XenoMax™/SLAM™ technologies (Babcook et al. A novelstrategy for generating monoclonal antibodies from single, isolatedlymphocytes producing antibodies of defined specificities. Proc NatlAcad Sci USA. 93(15):7843-8 (1996), and U.S. Pat. No. 5,627,052).Antibodies identified that bound to EGFRvIII were screened in a seriesof assays to ascertain specific recognition of EGFRvIII. Through thisprocess, panels of human monoclonal antibodies that bound to and werespecific for EGFRvIII were generated, isolated, and characterized.Subsequent epitope mapping demonstrated unique but overlappingspecificities. All antibodies were further evaluated in vitro for theirability to be internalized by cells for the purpose of deliveringcytotoxic drugs to cells. Antibodies demonstrating efficient drugdelivery were directly conjugated with a cytotoxic drug and examined fortheir ability to kill tumor cells expressing EGFRvIII in vitro and invivo. These studies provide the basis for the next generation ofantibody drug conjugates for treating cancer in patients whose tumorharbor specific genetic lesions.

Through the processes described above, panels of fully humananti-EGFRvIII antibodies were generated. Using the hybridoma approach,several antibodies, including antibody 13.1, 13.2, 13.3, and 13.4 thatwere positive on ELISA for binding with the PEP3, were generated withlimited cross-reactivity with wild type EGFR. Out of these, antibody13.1 (and, particularly, its subclone 13.1.2) was selected for furtherresearch and development. Using the XenoMax approach a panel ofantibodies, including antibody 131, 139, 250, and 095, were generatedthat were highly specific for binding with the pep3 oligonucleotide andhad limited cross-reactivity with wild type EGFR. Of these, the 131antibody has very interesting properties. The sequences for each of theantibodies are displayed in FIGS. 4-7 (SEQ ID NO: 1-33 and 141-144). Acomparison of the sequences and binding abilities of the variousantibodies was made and the results are displayed in FIGS. 4-10. As canbe seen in FIGS. 9A-9L, and FIGS. 10A-10D antibodies 131, 139, and13.1.2 all demonstrated superior selectivity for EGFRvIII expressingcells (H1477) as compared to ABX-EGF. Some of the results are shown ingraph form in FIGS. 9M-9P, which demonstrates that at least two of theantibodies, 13.1.2 and 131 demonstrated superior specificity forEGFRvIII expressing cells compared to simply EGFRvIII cells. Finally,based on predicted structural models, variants of the antibodies weremade in order to obtain antibodies with altered binding characteristics.

Further, antibodies of the invention are highly useful for the screeningof other antibodies that bind to the same or similar epitopes.Antibodies of the invention can be utilized in cross competition studiesfor the elucidation of other antibodies that are expected to have thesame or improved effects with respect to characteristics of theantigen-antibody complex that is formed.

Each of the 131 antibody and the 13.1.2 possessed very high affinitiesfor EGFRvIII, were internalized well by cells, and appeared highlyeffective in cell killing when conjugated to toxins. Intriguingly, bothof the antibodies, despite having been generated in differentimmunizations of XenoMouse mice, and utilizing different technologies,were derived from very similar germline genes. Based upon epitopemapping work, however, each of the antibodies appears to bind toslightly different epitopes on the EGFRvIII molecule and have slightlydifferent residues on EGFRvIII that are essential for binding. Theseresults indicate that the germline gene utilization is of importance tothe generation of antibody therapeutics targeting EGFRvIII and thatsmall changes can modify the binding and effects of the antibody in waysthat allow for the further design of antibodies and other therapeuticsbased upon these structural findings.

Antibodies that bind to the same epitope as, or compete for bindingwith, the 13.1.2 and 131 antibodies are highly desirable. As discussedin more detail below, through Alanine scanning on SPOTs arrays importantresidues for binding of certain antibodies have been elucidated.Accordingly, antibodies that share critical binding residues are alsohighly desirable.

Definitions

Unless otherwise defined, scientific and technical terms used hereinshall have the meanings that are commonly understood by those ofordinary skill in the art. Further, unless otherwise required bycontext, singular terms shall include pluralities and plural terms shallinclude the singular. Generally, nomenclatures utilized in connectionwith, and techniques of, cell and tissue culture, molecular biology, andprotein and oligo- or polynucleotide chemistry and hybridizationdescribed herein are those well known and commonly used in the art.Standard techniques are used for recombinant DNA, oligonucleotidesynthesis, and tissue culture and transformation (e.g., electroporation,lipofection). Enzymatic reactions and purification techniques areperformed according to manufacturer's specifications or as commonlyaccomplished in the art or as described herein. The foregoing techniquesand procedures are generally performed according to conventional methodswell known in the art and as described in various general and morespecific references that are cited and discussed throughout the presentspecification. See e.g., Sambrook et al. Molecular Cloning: A LaboratoryManual (2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y., 1989), which is incorporated herein by reference. Thenomenclatures utilized in connection with, and the laboratory proceduresand techniques of, analytical chemistry, synthetic organic chemistry,and medicinal and pharmaceutical chemistry described herein are thosewell known and commonly used in the art. Standard techniques are usedfor chemical syntheses, chemical analyses, pharmaceutical preparation,formulation, and delivery, and treatment of patients.

The term “isolated polynucleotide” as used herein shall mean apolynucleotide of genomic, cDNA, or synthetic origin or some combinationthereof, which by virtue of its origin the “isolated polynucleotide” (1)is not associated with all or a portion of a polynucleotide in which the“isolated polynucleotide” is found in nature, (2) is operably linked toa polynucleotide which it is not linked to in nature, or (3) does notoccur in nature as part of a larger sequence.

The term “isolated protein” referred to herein means a protein of cDNA,recombinant RNA, or synthetic origin or some combination thereof, whichby virtue of its origin, or source of derivation, the “isolated protein”(1) is not associated with proteins found in nature, (2) is free ofother proteins from the same source, e.g. free of murine proteins, (3)is expressed by a cell from a different species, or (4) does not occurin nature.

The term “polypeptide” is used herein as a generic term to refer tonative protein, fragments, or analogs of a polypeptide sequence. Hence,native protein, fragments, and analogs are species of the polypeptidegenus. Preferred polypeptides in accordance with the invention comprisethe human heavy chain immunoglobulin molecules and the human kappa lightchain immunoglobulin molecules, as well as antibody molecules formed bycombinations comprising the heavy chain immunoglobulin molecules withlight chain immunoglobulin molecules, such as the kappa light chainimmunoglobulin molecules or lambda light chain immunoglobulin molecules,and vice versa, as well as fragments and analogs thereof.

The term “naturally-occurring” as used herein as applied to an objectrefers to the fact that an object can be found in nature. For example, apolypeptide or polynucleotide sequence that is present in an organism(including viruses) that can be isolated from a source in nature andwhich has not been intentionally modified by man in the laboratory orotherwise is naturally-occurring.

The term “operably linked” as used herein refers to positions ofcomponents so described are in a relationship permitting them tofunction in their intended manner. A control sequence “operably linked”to a coding sequence is ligated in such a way that expression of thecoding sequence is achieved under conditions compatible with the controlsequences.

The term “control sequence” as used herein refers to polynucleotidesequences which are necessary to effect the expression and processing ofcoding sequences to which they are ligated. The nature of such controlsequences differs depending upon the host organism; in prokaryotes, suchcontrol sequences generally include promoter, ribosomal binding site,and transcription termination sequence; in eukaryotes, generally, suchcontrol sequences include promoters and transcription terminationsequence. The term “control sequences” is intended to include, at aminimum, all components whose presence is essential for expression andprocessing, and can also include additional components whose presence isadvantageous, for example, leader sequences and fusion partnersequences.

The term “polynucleotide” as referred to herein means a polymeric formof nucleotides of at least 10 bases in length, either ribonucleotides ordeoxynucleotides or a modified form of either type of nucleotide. Theterm includes single and double stranded forms of DNA.

The term “oligonucleotide” referred to herein includes naturallyoccurring, and modified nucleotides linked together by naturallyoccurring, and non-naturally occurring oligonucleotide linkages.Oligonucleotides are a polynucleotide subset generally comprising alength of 200 bases or fewer. Preferably oligonucleotides are 10 to 60bases in length and most preferably 12, 13, 14, 15, 16, 17, 18, 19, or20 to 40 bases in length. Oligonucleotides are usually single stranded,e.g. for probes; although oligonucleotides may be double stranded, e.g.for use in the construction of a gene mutant. Oligonucleotides of theinvention can be either sense or antisense oligonucleotides.

The term “naturally occurring nucleotides” referred to herein includesdeoxyribonucleotides and ribonucleotides. The term “modifiednucleotides” referred to herein includes nucleotides with modified orsubstituted sugar groups and the like. The term “oligonucleotidelinkages” referred to herein includes oligonucleotides linkages such asphosphorothioate, phosphorodithioate, phosphoroselenoate,phosphorodiselenoate, phosphoroanilothioate, phosphoraniladate,phosphoroamidate, and the like. See e.g., LaPlanche et al. Nucl. AcidsRes. 14:9081 (1986); Stec et al. J. Am. Chem. Soc. 106:6077 (1984);Stein et al. Nucl. Acids Res. 16:3209 (1988); Zon et al. Anti-CancerDrug Design 6:539 (1991); Zon et al. Oligonucleotides and Analogues: APractical Approach, pp. 87-108 (F. Eckstein, Ed., Oxford UniversityPress, Oxford England (1991)); Stec et al. U.S. Pat. No. 5,151,510;Uhlmann and Peyman Chemical Reviews 90:543 (1990), the disclosures ofwhich are hereby incorporated by reference. An oligonucleotide caninclude a label for detection, if desired.

The term “variant” as used herein, is a polypeptide, polynucleotide, ormolecule that differs from the recited polypeptide or polynucleotide,but only such that the activity of the protein is not detrimentallyaltered. There may be variants of epitopes. There may be variants ofantibodies. In a preferred embodiment, the ability of a protein variantto bind to the epitope is not detrimentally altered. In one embodiment,the protein variant can bind with 10-500% of the ability of the wildtype mAb. For example, the protein variant can bind with 10%, 50%, 110%,500%, or greater than 500% of the ability of the wild type mAb. In oneembodiment, the range of binding abilities between 10-500% is inlcuded.Binding ability may be reflected in many ways, including, but notlimited to the k_(a), k_(a), or K_(D) of the variant to an epitope. Inone preferred embodiment, the epitope is one described in the presentspecification.

In one embodiment, variant antibodies can differ from the wild-typesequence by substitution, deletion or addition of five amino acids orfewer. Such variants may generally be identified by modifying one of thedisclosed polypeptide sequences, and evaluating the binding propertiesof the modified polypeptide using, for example, the representativeprocedures described herein. In another embodiment, polypeptide variantspreferably exhibit at least about 70%, more preferably at least about90% and most preferably at least about 95% identity to the identifiedpolypeptides. Preferrably, the variant differs only in conservativesubstitutions and/or modifications. Variant proteins include those thatare structurally similar and those that are functionally equivalent tothe protein structures described in the present specification. Inanother embodiment, the protein is a variant if it is functionallyequivalent to the proteins described in this specification, so long asthe paratope of variant is similar to the paratopes described in thespecification. In one embodiment, any substance with a shape that issimilar to the paratope described in FIG. 11 is a variant. In oneembodiment, any substance with a shape that is similar to the paratopedescribed in FIG. 12 is a variant. In one embodiment, any substance thathas a shape that is similar to the interaction surface described inFIGS. 13A and 13B is a variant.

In one embodiment, the antibody is a variant if the nucleic acidsequence can selectively hybridize to wild-type sequence under stringentconditions. In one embodiment, suitable moderately stringent conditionsinclude prewashing in a solution of 5×SSC; 0.5% SDS, 1.0 mM EDTA (pH8:0); hybridizing at 50° C.−65° C., 5×SSC, overnight or, in the event ofcross-species homology, at 45° C. with 0.5×SSC; followed by washingtwice at 65° C. for 20 minutes with each of 2×, 0.5× and 0.2×SSCcontaining 0.1% SDS. Such hybridizing DNA sequences are also within thescope of this invention, as are nucleotide sequences that, due to codedegeneracy, encode an antibody polypeptide that is encoded by ahybridizing DNA sequence. The term “selectively hybridize” referred toherein means to detectably and specifically bind. Polynucleotides,oligonucleotides and fragments thereof in accordance with the inventionselectively hybridize to nucleic acid strands under hybridization andwash conditions that minimize appreciable amounts of detectable bindingto nonspecific nucleic acids. High stringency conditions can be used toachieve selective hybridization conditions as known in the art anddiscussed herein. Generally, the nucleic acid sequence homology betweenthe polynucleotides, oligonucleotides, and fragments of the inventionand a nucleic acid sequence of interest will be at least 80%, and moretypically with preferably increasing homologies of at least 85%, 90%,95%, 99%, and 100%. Two amino acid sequences are homologous if there isa partial or complete identity between their sequences. For example, 85%homology means that 85% of the amino acids are identical when the twosequences are aligned for maximum matching. Gaps (in either of the twosequences being matched) are allowed in maximizing matching; gap lengthsof 5 or less are preferred with 2 or less being more preferred.Alternatively and preferably, two protein sequences (or polypeptidesequences derived from them of at least 30 amino acids in length) arehomologous, as this term is used herein, if they have an alignment scoreof at more than 5 (in standard deviation units) using the program ALIGNwith the mutation data matrix and a gap penalty of 6 or greater. SeeDayhoff, M. O., in Atlas of Protein Sequence and Structure, pp. 101-110(Volume 5, National Biomedical Research Foundation (1972)) andSupplement 2 to this volume, pp. 1-10. The two sequences or partsthereof are more preferably homologous if their amino acids are greaterthan or equal to 50% identical when optimally aligned using the ALIGNprogram. The term “corresponds to” is used herein to mean that apolynucleotide sequence is homologous (i.e., is identical, not strictlyevolutionarily related) to all or a portion of a referencepolynucleotide sequence, or that a polypeptide sequence is identical toa reference polypeptide sequence. In contradistinction, the term“complementary to” is used herein to mean that the complementarysequence is homologous to all or a portion of a reference polynucleotidesequence. For illustration, the nucleotide sequence “TATAC” correspondsto a reference sequence “TATAC” and is complementary to a referencesequence “GTATA”.

The following terms are used to describe the sequence relationshipsbetween two or more polynucleotide or amino acid sequences: “referencesequence”, “comparison window”, “sequence identity”, “percentage ofsequence identity”, and “substantial identity”. A “reference sequence”is a defined sequence used as a basis for a sequence comparison; areference sequence may be a subset of a larger sequence, for example, asa segment of a full-length cDNA or gene sequence given in a sequencelisting or may comprise a complete cDNA or gene sequence. Generally, areference sequence is at least 18 nucleotides or 6 amino acids inlength, frequently at least 24 nucleotides or 8 amino acids in length,and often at least 48 nucleotides or 16 amino acids in length. Since twopolynucleotides or amino acid sequences may each (1) comprise a sequence(i.e., a portion of the complete polynucleotide or amino acid sequence)that is similar between the two molecules, and (2) may further comprisea sequence that is divergent between the two polynucleotides or aminoacid sequences, sequence comparisons between two (or more) molecules aretypically performed by comparing sequences of the two molecules over a“comparison window” to identify and compare local regions of sequencesimilarity. A “comparison window”, as used herein, refers to aconceptual segment of at least 18 contiguous nucleotide positions or 6amino acids wherein a polynucleotide sequence or amino acid sequence maybe compared to a reference sequence of at least 18 contiguousnucleotides or 6 amino acid sequences and wherein the portion of thepolynucleotide sequence in the comparison window may comprise additions,deletions, substitutions, and the like (i.e., gaps) of 20 percent orless as compared to the reference sequence (which does not compriseadditions or deletions) for optimal alignment of the two sequences.Optimal alignment of sequences for aligning a comparison window may beconducted by the local homology algorithm of Smith and Waterman Adv.Appl. Math. 2:482 (1981), by the homology alignment algorithm ofNeedleman and Wunsch J. Mol. Biol. 48:443 (1970), by the search forsimilarity method of Pearson and Lipman Proc. Natl. Acad. Sci. (U.S.A.)85:2444 (1988); by computerized implementations of these algorithms(GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics SoftwarePackage Release 7.0, (Genetics Computer Group, 575 Science Dr., Madison,Wis.), Geneworks, or MacVector software packages), or by inspection, andthe best alignment (i.e., resulting in the highest percentage ofhomology over the comparison window) generated by the various methods isselected.

The term “sequence identity” means that two polynucleotide or amino acidsequences are identical (i.e., on a nucleotide-by-nucleotide orresidue-by-residue basis) over the comparison window. The term“percentage of sequence identity” is calculated by comparing twooptimally aligned sequences over the window of comparison, determiningthe number of positions at which the identical nucleic acid base (e.g.,A, T, C, G, U, or I) or residue occurs in both sequences to yield thenumber of matched positions, dividing the number of matched positions bythe total number of positions in the comparison window (i.e., the windowsize), and multiplying the result by 100 to yield the percentage ofsequence identity. The terms “substantial identity” as used hereindenotes a characteristic of a polynucleotide or amino acid sequence,wherein the polynucleotide or amino acid comprises a sequence that hasat least 85 percent sequence identity, preferably at least 90 to 95percent sequence identity, more usually at least 99 percent sequenceidentity as compared to a reference sequence over a comparison window ofat least 18 nucleotide (6 amino acid) positions, frequently over awindow of at least 24-48 nucleotide (8-16 amino acid) positions, whereinthe percentage of sequence identity is calculated by comparing thereference sequence to the sequence which may include deletions oradditions which total 20 percent or less of the reference sequence overthe comparison window. The reference sequence may be a subset of alarger sequence. Amino acids or nucleic acids with substantial identityto the wild-type protein or nucleic acid are examples of variants of thewild-type protein or nucleic acid.

As used herein, the twenty conventional amino acids and theirabbreviations follow conventional usage. See Immunology—A Synthesis(2^(nd) Edition, E. S. Golub and D. R. Gren, Eds., Sinauer Associates,Sunderland, Mass. (1991)), which is incorporated herein by reference.Stereoisomers (e.g., D-amino acids) of the twenty conventional aminoacids, unnatural amino acids such as α-, α-disubstituted amino acids,N-alkyl amino acids, lactic acid, and other unconventional amino acidsmay also be suitable components for polypeptides of the presentinvention. Examples of unconventional amino acids include:4-hydroxyproline, γ-carboxyglutamate, ε-N,N,N-trimethyllysine,ε-N-acetyllysine, O-phosphoserine, N-acetylserine, N-formylmethionine,3-methylhistidine, 5-hydroxylysine, σ-N-methylarginine, and othersimilar amino acids and imino acids (e.g., 4-hydroxyproline). In thepolypeptide notation used herein, the left-hand direction is the aminoterminal direction and the right-hand direction is the carboxy-terminaldirection, in accordance with standard usage and convention.

Similarly, unless specified otherwise, the left-hand end ofsingle-stranded polynucleotide sequences is the 5′ end; the left-handdirection of double-stranded polynucleotide sequences is referred to asthe 5′ direction. The direction of 5′ to 3′ addition of nascent RNAtranscripts is referred to as the transcription direction; sequenceregions on the DNA strand having the same sequence as the RNA and whichare 5′ to the 5′ end of the RNA transcript are referred to as “upstreamsequences”; sequence regions on the DNA strand having the same sequenceas the RNA and which are 3′ to the 3′ end of the RNA transcript arereferred to as “downstream sequences”.

As applied to polypeptides, the term “substantial identity” means thattwo peptide sequences, when optimally aligned, such as by the programsGAP or BESTFIT using default gap weights, share at least 80 percentsequence identity, preferably at least 90 percent sequence identity,more preferably at least 95 percent sequence identity, and mostpreferably at least 99 percent sequence identity. Preferably, residuepositions which are not identical differ by conservative amino acidsubstitutions. Conservative amino acid substitutions refer to theinterchangeability of residues having similar side chains. For example,a group of amino acids having aliphatic side chains is glycine, alanine,valine, leucine, and isoleucine; a group of amino acids havingaliphatic-hydroxyl side chains is serine and threonine; a group of aminoacids having amide-containing side chains is asparagine and glutamine; agroup of amino acids having aromatic side chains is phenylalanine,tyrosine, and tryptophan; a group of amino acids having basic sidechains is lysine, arginine, and histidine; and a group of amino acidshaving sulfur-containing side chains is cysteine and methionine.Preferred conservative amino acids substitution groups are:valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine,alanine-valine, glutamic-aspartic, and asparagine-glutamine.Polypeptides with substantial identity can be variants.

Variant proteins also include proteins with minor variations. Asdiscussed herein, minor variations in the amino acid sequences ofantibodies or immunoglobulin molecules are contemplated as beingencompassed by the present invention, providing that the variations inthe amino acid sequence maintain at least 75%, more preferably at least80%, 90%, 95%, and most preferably 99%. In particular, conservativeamino acid replacements are contemplated.

Conservative replacements are those that take place within a family ofamino acids that are related in their side chains. Genetically encodedamino acids are generally divided into families: (1) acidic=aspartate,glutamate; (2) basic=lysine, arginine, histidine; (3) non-polar=alanine,valine, leucine, isoleucine, proline, phenylalanine, methionine,tryptophan; and (4) uncharged polar=glycine, asparagine, glutamine,cysteine, serine, threonine, tyrosine. More preferred families are:serine and threonine are aliphatic-hydroxy family; asparagine andglutamine are an amide-containing family; alanine, valine, leucine andisoleucine are an aliphatic family; and phenylalanine, tryptophan, andtyrosine are an aromatic family. For example, it is reasonable to expectthat an isolated replacement of a leucine with an isoleucine or valine,an aspartate with a glutamate, a threonine with a serine, or a similarreplacement of an amino acid with a structurally related amino acid willnot have a major effect on the binding or properties of the resultingmolecule, especially if the replacement does not involve an amino acidwithin a framework site. Whether an amino acid change results in afunctional peptide can readily be determined by assaying the specificactivity of the polypeptide derivative. Assays are described in detailherein. Fragments or analogs of antibodies or immunoglobulin moleculescan be readily prepared by those of ordinary skill in the art. Preferredamino- and carboxy-termini of fragments or analogs occur near boundariesof functional domains. Structural and functional domains can beidentified by comparison of the nucleotide and/or amino acid sequencedata to public or proprietary sequence databases. Preferably,computerized comparison methods are used to identify sequence motifs orpredicted protein conformation domains that occur in other proteins ofknown structure and/or function. Methods to identify protein sequencesthat fold into a known three-dimensional structure are known. Bowie etal. Science 253:164 (1991). Thus, the foregoing examples demonstratethat those of skill in the art can recognize sequence motifs andstructural conformations that may be used to define structural andfunctional domains in accordance with the antibodies described herein.

Preferred amino acid substitutions are those which: (1) reducesusceptibility to proteolysis, (2) reduce susceptibility to oxidation,(3) alter binding affinity for forming protein complexes, (4) alterbinding affinities, and (4) confer or modify other physicochemical orfunctional properties of such analogs. Analogs can include variousmuteins of a sequence other than the naturally-occurring peptidesequence. For example, single or multiple amino acid substitutions(preferably conservative amino acid substitutions) may be made in thenaturally-occurring sequence (preferably in the portion of thepolypeptide outside the domain(s) forming intermolecular contacts. Aconservative amino acid substitution should not substantially change thestructural characteristics of the parent sequence (e.g., a replacementamino acid should not tend to break a helix that occurs in the parentsequence, or disrupt other types of secondary structure thatcharacterizes the parent sequence). Examples of art-recognizedpolypeptide secondary and tertiary structures are described in Proteins,Structures and Molecular Principles (Creighton, Ed., W. H. Freeman andCompany, New York (1984)); Introduction to Protein Structure (C. Brandenand J. Tooze, eds., Garland Publishing, New York, N.Y. (1991)); andThornton et at. Nature 354:105 (1991), which are each incorporatedherein by reference.

The term “polypeptide fragment” as used herein refers to a polypeptidethat has an amino-terminal and/or carboxy-terminal deletion, but wherethe remaining amino acid sequence is identical to the correspondingpositions in the naturally-occurring sequence deduced, for example, froma full-length cDNA sequence. Fragments typically are at least 5, 6, 8 or10 amino acids long, preferably at least 14 amino acids long, morepreferably at least 20 amino acids long, usually at least 50 amino acidslong, and even more preferably at least 70 amino acids long. The term“analog” as used herein refers to polypeptides which are comprised of asegment of at least 25 amino acids that has substantial identity to aportion of a deduced amino acid sequence. Analogs typically are at least20 amino acids long, preferably at least 50 amino acids long or longer,and can often be as long as a full-length naturally-occurringpolypeptide. Both fragments and analogs are forms of variants

Peptide analogs are commonly used in the pharmaceutical industry asnon-peptide drugs with properties analogous to those of the templatepeptide. These types of non-peptide compound are termed “peptidemimetics” or “peptidomimetics”. Fauchere, J. Adv. Drug Res. 15:29(1986); Veber and Freidinger TINS p. 392 (1985); and Evans et al. J.Med. Chem. 30:1229 (1987), which are incorporated herein by reference.Such compounds are often developed with the aid of computerizedmolecular modeling. Peptide mimetics that are structurally similar totherapeutically useful peptides may be used to produce an equivalenttherapeutic or prophylactic effect. Generally, peptidomimetics arestructurally similar to a paradigm polypeptide (i.e., a polypeptide thathas a biochemical property or pharmacological activity), such as humanantibody, but have one or more peptide linkages optionally replaced by alinkage selected from the group consisting of: —CH₂NH—, —CH₂S—,—CH₂—CH₂—, —CH═CH-(cis and trans), —COCH₂—, —CH(OH)CH₂—, and —CH₂SO—, bymethods well known in the art. Systematic substitution of one or moreamino acids of a consensus sequence with a D-amino acid of the same type(e.g., D-lysine in place of L-lysine) may be used to generate morestable peptides. In addition, constrained peptides comprising aconsensus sequence or a substantially identical consensus sequencevariation may be generated by methods known in the art (Rizo andGierasch Ann. Rev. Biochem. 61:387 (1992), incorporated herein byreference); for example, by adding internal cysteine residues capable offorming intramolecular disulfide bridges which cyclize the peptide.Peptide mimetics and peptidomimetics are both forms of variants.

“Antibody” or “antibody peptide(s)” refer to an intact antibody, or abinding fragment thereof that competes with the intact antibody forspecific binding. Binding fragments are produced by recombinant DNAtechniques, or by enzymatic or chemical cleavage of intact antibodies.Binding fragments include Fab, Fab′, F(ab)₂, Fv, and single-chainantibodies. An antibody other than a “bispecific” or “bifunctional”antibody is understood to have each of its binding sites identical. Anantibody substantially inhibits adhesion of a receptor to acounterreceptor when an excess of antibody reduces the quantity ofreceptor bound to counterreceptor by at least about 20%, 40%, 60% or80%, and more usually greater than about 85% (as measured in an in vitrocompetitive binding assay).

The term “epitope” includes any protein determinant capable of specificbinding to an immunoglobulin or T-cell receptor or otherwise interactingwith a molecule. Epitopic determinants generally consist of chemicallyactive surface groupings of molecules such as amino acids orcarbohydrate or sugar side chains and generally have specificthree-dimensional structural characteristics, as well as specific chargecharacteristics. An epitope may be “linear” or “conformational.” In alinear epitope, all of the points of interaction between the protein andthe interacting molecule (such as an antibody) occur linearally alongthe primary amino acid sequence of the protein. In a conformationalepitope, the points of interaction occur across amino acid residues onthe protein that are separated from one another. An antibody is said tospecifically bind an antigen when the dissociation constant is ≤1M,preferably ≤100 nM and more preferably ≤10 nM, and even more preferably1 nM. Once a desired epitope on an antigen is determined, it is possibleto generate antibodies to that epitope, e.g., using the techniquesdescribed in the present invention. Alternatively, during the discoveryprocess, the generation and characterization of antibodies may elucidateinformation about desirable epitopes. From this information, it is thenpossible to competitively screen antibodies for binding to the sameepitope. An approach to achieve this is to conduct cross-competitionstudies to find antibodies that competively bind with one another, e.g.,the antibodies compete for binding to the antigen. A high throughputprocess for “binning” antibodies based upon their cross-competition isdescribed in International Patent Application No. WO 03/48731. As willbe appreciated by one of skill in the art, practically anything to whichan antibody can specificially bind could be an epitope. An epitope cancomprises those residues to which the antibody binds. In one embodiment,the epitope is the EGFRvIII epitope. In a more preferred embodiment, theepitope is that described in Example 4 of this specification. In oneembodiment, the epitope is the epitope described in Example 14. In oneembodiment, the epitope comprises the sequence LEEKKGNYVVTD (SEQ ID NO:59). In one embodiment, the epitope comprises the sequence EEKKGNYVVT(SEQ ID NO: 57). In one embodiment, the epitope comprises the sequenceEKNY (SEQ ID NO: 60). In one embodiment, the epitope comprises thesequence EEKGN (SEQ ID NO: 61). One of skill in the art will appreciatethat these need not be actually assembled in this order on a singlepeptide, rather, these are the residues that form the eptiope whichinteracts with the paratope. As will be appreciated by one of skill inthe art, the space that is occupied by a residue or side chain thatcreates the shape of a molecule helps to determine what an epitope is.Likewise, any functional groups associated with the epitope, van derWaals interactions, degree of mobility of side chains, etc. can alldetermine what an epitope actually is. Thus an epitope may also includeenergetic interactions.

The term “paratope” is meant to describe the general structure of abinding region that determines binding to an epitope. This structureinfluences whether or not and in what manner the binding region mightbind to an epitope. Paratope can refer to an antigenic site of anantibody that is responsible for an antibody or fragment thereof, tobind to an antigenic determinant. Paratope also refers to the idiotopeof the antibody, and the complementary determining region (CDR) regionthat binds to the epitope. In one embodiment, the paratope is the regionof the antibody that is L1 10, L2 30, L3 50, H1 20, H2 40, and H3 60 inFIG. 11. In one embodiment, the paratope is the region of the antibodythat comprises the CDR sequences in Example 16 for L1, L2, L3, H1, H2,and H3. In one embodiment, the paratope is the region of the antibodythat is L1 110, L2 130, L3 150, H1 120, H2 140, and H3 160 in FIG. 12.In one embodiment, the paratope is the region of the antibody thatcomprises the CDR sequences in Example 18 for L 1, L2, L3, H1, H2, andH3. In one embodiment, the paratope comprises the sequences listed inExample 18. In one embodiment, the paratope comprises the residues thatinteract with the epitope, as shown in FIG. 13A and FIG. 13B. The solidblack structure is the peptide structure. In one embodiment, theparatope comprises residue Tyr172Arg of the 13.1.2 mAb. In oneembodiment, the paratope of the 13.1.2 mAb comprises at least oneresidue selected from the group consisting of: Tyr 172Arg, Arg101Glu,Leu99Asn, Leu99His, Arg101 Asp, Leu217Gln, Leu99Thr, Leu217Asn,Arg101Gln, and Asn35Gly. As will be appreciated by one of skill in theart, the paratope of any antibody, or variant thereof, can be determinedin the manner set forth by the present application. Residues areconsidered “important” if they are predicted to contribute 10% of thebinding energy. In one embodiment, residues are considered “important”if they are predicted to contribute 2% of the binding energy. In oneembodiment, residues are considered “important” if they are predicted tocontribute 50% of the binding energy. In one embodiment, residues areconsidered “important” if they are predicted to interact with thesurface of the epitope, or the surface of the paratope. In oneembodiment, residues are considered “important” if changing the residueresults in a loss in binding.

The terms “specifically” or “preferrentially” binds to, or similarphrases are not meant to denote that the antibody exclusively binds tothat epitope. Rather, what is meant is that the antibody, or variantthereof, can bind to that epitope, to a higher degree than the antibodybinds to at least one other substance to which the antibody is exposedto. In one embodiment, the specifically binding antibody will bind tothe EGFRvIII protein with an affinity greater than (more tightly, orlower K_(D)) it will to the EGFR protein. For example, the specificallybinding antibody will bind more tightly by at least a minimal increaseto 1, 1-2, 2-5, 5-10, 10-20, 20-30, 30-50, 50-70, 70-90, 90-120,120-150, 150-200, 200-300, 300-500, 500-1000 percent or more.

The shorthand of amino acid, number, amino acid, e.g., Leu217Gln,denotes a mutation at the numbered amino acid, from the first aminoacid, to the second amino acid. Thus, Tyr172Arg would mean that whilethe wild type protein has a tyrosine at position 172, the mutant has anarginine at position 172.

The term “agent” is used herein to denote a chemical compound, a mixtureof chemical compounds, a biological macromolecule, or an extract madefrom biological materials.

“Mammal” when used herein refers to any animal that is considered amammal. Preferably, the mammal is human.

Digestion of antibodies with the enzyme, papain, results in twoidentical antigen-binding fragments, known also as “Fab” fragments, anda “Fc” fragment, having no antigen-binding activity but having theability to crystallize. Digestion of antibodies with the enzyme, pepsin,results in the a F(ab′)₂ fragment in which the two arms of the antibodymolecule remain linked and comprise two-antigen binding sites. TheF(ab′)₂ fragment has the ability to crosslink antigen.

“Fv” when used herein refers to the minimum fragment of an antibody thatretains both antigen-recognition and antigen-binding sites. Thesefragments can also be considered variants of the antibody.

“Fab” when used herein refers to a fragment of an antibody whichcomprises the constant domain of the light chain and the CH1 domain ofthe heavy chain.

The term “mAb” refers to monoclonal antibody.

The description of XenoMax method generated antibody sequences is codedas follows: “AB”-referring to antibody, “EGFRvIII”-referring toantibody's binding specificity, “X” referring to XenoMouse mousederived, “G1”-referring to IgG1 isotype or “G2” referring to IgG2isotype, the last three digits refer to the single cell number fromwhich the antibody was derived, for example: AB-EGFRvIII-XG1-095 wouldbe an antibody with binding specificity to EGFRvIII from XenoMouse mouseof a IgG1 isotype and cell number 95.

The term “SC” refers to single cell and a particular XenoMax methodderived antibody may be referred to as SC followed by three digits, orjust three digits, referring to the single cell number from which theantibody was derived herein.

The description of hybridoma derived antibody sequences is coded asfollows: “AB”-referring to antibody, “EGFRvIII”-refers to the antibody'sbinding specificity, “X” refers to XenoMouse mouse derived, “G1”-refersto IgG1 isotype or “G2” refers to IgG2 isotype, “K” refers to kappa, “L′refers to lambda. The last three digits referring to the clone fromwhich the antibody was derived, for example: AB-EGFRvIII-XG1K-13.1.2

“Label” or “labeled” as used herein refers to the addition of adetectable moiety to a polypeptide, for example, a radiolabel,fluorescent label, enzymatic label chemiluminescent labeled or abiotinyl group. Radioisotopes or radionuclides may include ³H, ¹⁴C, ¹⁵N,³⁵S, ⁹⁰Y, ⁹⁹Tc, ¹¹¹In, ¹²⁵I, ¹³¹I, fluorescent labels may includerhodamine, lanthanide phosphors or FITC and enzymatic labels may includehorseradish peroxidase, β-galactosidase, luciferase, alkalinephosphatase.

The term “pharmaceutical agent or drug” as used herein refers to achemical compound or composition capable of inducing a desiredtherapeutic effect when properly administered to a patient. Otherchemistry terms herein are used according to conventional usage in theart, as exemplified by The McGraw-Hill Dictionary of Chemical Terms(Parker, S., Ed., McGraw-Hill, San Francisco (1985)), (incorporatedherein by reference).

As used herein, “substantially pure” means an object species is thepredominant species present (i.e., on a molar basis it is more abundantthan any other individual species in the composition), and preferably asubstantially purified fraction is a composition wherein the objectspecies comprises at least about 50 percent (on a molar basis) of allmacromolecular species present. Generally, a substantially purecomposition will comprise more than about 80 percent of allmacromolecular species present in the composition, more preferably morethan about 85%, 90%, 95%, 99%, and 99.9%. Most preferably, the objectspecies is purified to essential homogeneity (contaminant species cannotbe detected in the composition by conventional detection methods)wherein the composition consists essentially of a single macromolecularspecies.

The term “patient” includes human and veterinary subjects.

The term “SLAM® Technology” refers to the “Selected Lymphocyte AntibodyMethod” (Babcook et al., Proc. Natl. Acad. Sci. USA, i93:7843-7848(1996), and Schrader, U.S. Pat. No. 5,627,052, both of which areincorporated by reference in their entirety).

The term “XenoMax™” refers to the use of SLAM Technology with XenoMouse®mice (as described below).

Antibody Structure

The basic antibody structural unit is known to comprise a tetramer. Eachtetramer is composed of two identical pairs of polypeptide chains, eachpair having one “light” (about 25 kDa) and one “heavy” chain (about50-70 kDa). The amino-terminal portion of each chain includes a variableregion of about 100 to 110 or more amino acids primarily responsible forantigen recognition. The carboxy-terminal portion of each chain definesa constant region primarily responsible for effector function. Humanlight chains are classified as kappa and lambda light chains. Heavychains are classified as mu, delta; gamma, alpha, or epsilon, and definethe antibody's isotype as IgM, IgD, IgG, IgA, and IgE, respectively.Within light and heavy chains, the variable and constant regions arejoined by a “J” region of about 12 or more amino acids, with the heavychain also including a “D” region of about 10 more amino acids. Seegenerally, Fundamental Immunology Ch. 7 (Paul, W., ed., 2nd ed. RavenPress, N.Y. (1989)) (incorporated by reference in its entirety for allpurposes). The variable regions of each light/heavy chain pair form theantibody binding site.

Thus, an intact antibody has two binding sites. Except in bifunctionalor bispecific antibodies, the two binding sites are the same.

The chains all exhibit the same general structure of relativelyconserved framework regions (FR) joined by three hyper variable regions,also called complementarity determining regions or CDRs. The CDRs fromthe two chains of each pair are aligned by the framework regions,enabling binding to a specific epitope. From N-terminal to C-terminal,both light and heavy chains comprise the domains FR1, CDR1, FR2, CDR2,FR3, CDR3 and FR4. The assignment of amino acids to each domain is inaccordance with the definitions of Kabat Sequences of Proteins ofImmunological Interest (National Institutes of Health, Bethesda, Md.(1987 and 1991)), or Chothia & Lesk J. Mol. Biol. 196:901-917 (1987);Chothia et al. Nature 342:878-883 (1989).

A bispecific or bifunctional antibody is an artificial hybrid antibodyhaving two different heavy/light chain pairs and two different bindingsites. Bispecific antibodies can be produced by a variety of methodsincluding fusion of hybridomas or linking of Fab′ fragments. See, e.g.,Songsivilai & Lachmann Clin. Exp. Immunol. 79: 315-321 (1990), Kostelnyet al. J. Immunol. 148:1547-1553 (1992). Production of bispecificantibodies can be a relatively labor intensive process compared withproduction of conventional antibodies and yields and degree of purityare generally lower for bispecific antibodies. Bispecific antibodies donot exist in the form of fragments having a single binding site (e.g.,Fab, Fab′, and Fv).

In addition to the general structural aspects of antibodies, the morespecific interaction between the paratope and the epitope may beexamined through structural approaches. In one embodiment, the structureof the CDRs form a paratope, through which an antibody is able to bindto an epitope. The structure of such a paratope may be determined in anumber of ways. Traditional structural examination approaches may beused, such as NMR or x-ray crystalography. These approaches may examinethe structure of the paratope alone, or while it is bound to theepitope. Alternatively, molecular models may be generated in silico. Astructure can be generated through homology modeling, aided with acommercial package, such as InsightII modeling package from Accelrys(San Diego, Calif.). Briefly, one can use the sequence of the antibodyto be examined to search against a database of proteins of knownstructures, such as the Protein Data Bank. After one identifieshomologous proteins with known structures, these homologous proteins areused as modeling templates. Each of the possible templates can bealigned, thus producing structure based sequence alignments amoung thetemplates. The sequence of the antibody with the unknown structure canthen be aligned with these templates to generate a molecular model forthe antibody with the unknown structure. As will be appreciated by oneof skill in the art, there are many alternative methods for generatingsuch structures in silico, any of which may be used. For instance, aprocess similar to the one described in Hardman et al., issued U.S. Pat.No. 5,958,708 employing QUANTA (Polygen Corp., Waltham, Mass.) and CHARM(Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J.,Swaminathan, S. and Karplus, M., 1983, J. Comp. Chem. 4:187) may be used(hereby incorporated in its entirety by reference).

Not only is the shape of the paratope important in determining whetherand how well a possible paratope will bind to an epitope, but theinteraction itself, between the epitope and the paratope is a source ofgreat information in the design of variant antibodies. As appreciated byone of skill in the art, there are a variety of ways in which thisinteraction can be studied. One way is to use the structural modelgenerated, perhaps as described above, and then to use a program such asInsightII (Accelrys, San Diego, Calif.), which has a docking module,which, among other things, is capable of performing a Monte Carlo searchon the conformational and orientational spaces between the paratope andits epitope. The result is that one is able to estimate where and howthe epitope interacts with the paratope. In one embodiment, only afragment, or variant, of the epitope is used to assist in determiningthe relevant interactions. In one embodiment, the entire epitope is usedin the modeling of the interaction between the paratope and the epitope.As will be appreciated by one of skill in the art, these two differentapproaches have different advantages and disadvantages. For instance,using only a fragment of the epitope allows for a more detailedexamination of the possible variations of each side chain, withouttaking huge amounts of time. On the other hand, by using only a fragmentof the epitope, or simply the epitope instead of the entire protein, itis possible that the characteristics of the epitope fragment may not bethe same as the characteristics for the whole epitope, thus possiblyincreasing the risk of being mislead during the computational modeling.In one embodiment, both approaches are used to a limited extent, inorder to cross check the results. In a preferred embodiment, if avariant of an epitope is used, it will be optimized so that the variantof the epitope comprises the most important residues of the epitope. Theidentity of the most important residues can be determined in any numberof ways, for instance as described in Examples 4 and 14 of the presentspecification.

Through the use of these generated structures, one is able to determinewhich residues are the most important in the interaction between theepitope and the paratope. Thus, in one embodiment, one is able toreadily select which residues to change in order to alter the bindingcharacteristics of the antibody. For instance, it may be apparent fromthe docking models that the side chains of certain residues in theparatope may sterically hinder the binding of the epitope, thus alteringthese residues to residues with smaller side chains may be beneficial.One can determine this in many ways. For example, one may simply look atthe two models and esitmate interactions based on functional groups andproximety. Alternatively, one may perform repeated pairings of epitopeand paratope, as described above, in order to obtain more favorableenergy interactions. One can also determine these interactions for avariety of variants of the antibody to determine alternative ways inwhich the antibody may bind to the epitope. One can also combine thevarious models to determine how one should alter the structure of theantibodies in order to obtain an antibody with the particularcharacteristics that are desired.

The models determined above can be tested through various techniques.For example, the interaction energy can determined with the programsdiscussed above in order to determine which of the variants to furtherexamine. Also, coulumbic and van der Waals interactions are used todetermine the interaction energies of the epitope and the variantparatopes. Also site directed mutagenesis is used to see if predictedchanges in antibody structure actually result in the desired changes inbinding characteristics. Alternatively, changes may be made to theepitope to verify that the models are correct or to determine generalbinding themes that may be occurring between the paratope and theepitope.

The above methods for modeling structures can be used to determine whatchanges in protein structure will result in particular desiredcharacteristics of an antibody. These methods can be used to determinewhat changes in protein structure will not result in the desiredcharacteristics.

As will be appreciated by one of skill in the art, while these modelswill provide the guidance necessary to make the antibodies and variantsthereof of the present embodiments, it may still be desirable to performroutine testing of the in silico models, perhaps through in vitrostudies. In addition, as will be apparent to one of skill in the art,any modification may also have additional side effects on the activityof the antibody. For instance, while any alteration predicted to resultin greater binding, may induce greater binding, it may also cause otherstructural changes which might reduce or alter the activity of theantibody. The determination of whether or not this is the case isroutine in the art and can be achieved in many ways. For Example, theactivity can be tested through an ELISA test, as in Example 21.Alternatively, the samples can be tested through the use of a surfaceplasmon resonance device.

Antibodies Binding, and Variant Antibodies for Superior Binding

In one embodiment, the models described above are used to increase thebinding ability of the antibody to its epitope. The antibody can bind tothe epitope more readily, and thus have a higher association constant(k_(a)). Alternatively, the antibody may dissociate from the epitopeslower, and thus have a lower dissociation constant (k_(J)), or theK_(D) of the epitope-paratope interaction can be smaller in value, thusmaking the extent of the binding between the epitope and paratopehigher.

In some embodiments, the variant antibodies are designed to bind withthe opposite characteristics. That is, the antibodies do not bind astightly or perhaps as quickly.

In other embodiments, the variant antibodies are not different in theirK_(D) from the wild-type antibodies, but the variant antibodies are morespecific for a particular epitope. This may mean that the paratopes ofthe designed antibodies have a lower risk of binding to other epitopes.The antibodies can have other characteristics that have been altered.For example, a variant may be more immune to nonspecific antibodybinding or may stay solvated in solution even when the antibody ispresent in high concentrations. Such a variant may be present in thediscussed antibodies. For instance, while the higher concentrations ofsome variant antibodies examined below resulted in slower bindingcomponents in Biacore experiments, for instance 13.1.2 mAb, certainvariants did not exhibit this slower component, even at the sameconcentrations, L217N-2.1, for example.

The variants predicted by the models determined above can be created andthen tested to determine if they actually bind with the desiredcharacteristics. Mutants with a greater total interaction energy withthe epitope can be selected for further testing. The interaction energycan be determined in a number of ways, one of which is described above.

These variants can be tested in a number of ways. Exemplary optionsinclude and are not limited to KinExA (e.g., Lackie, Issued U.S. Pat.No. 5,372,783, Dec. 13, 1994, herein incorporated in its entirety byreference)(Sapidyne Instruments Inc., ID, Boise), surface plasmonresonance (SPR)(e.g., BIACORE™ Biacore, Inc., Pistcataway, N.J.),stopped-flow fluorescence, resonant mirror, and fluorescencepolarization. Many of these options are able to not only record thedata, but also provide ready means for fitting the data to varioustheoretical curves and thus determine the k_(a), k_(d), and K_(D), aswell as other properties. It is important to note that the fitting ofthese curves to the resulting data is not without the possibility forsome variation. Because of this, the relevant association, dissociation,and equilibrium constants can be looked at, not only through these curvefitting mechanisms, but also in direct comparison with each other, andin light of the knowledge of one of skill in the art.

Human Antibodies and Humanization of Antibodies.

Human antibodies avoid some of the problems associated with antibodiesthat possess murine or rat variable and/or constant regions. Thepresence of such murine or rat derived proteins can lead to the rapidclearance of the antibodies or can lead to the generation of an immuneresponse against the antibody by a patient. In order to avoid theutilization of murine or rat derived antibodies, fully human antibodiescan be generated through the introduction of human antibody functioninto a rodent so that the rodent produces fully human antibodies.

The ability to clone and reconstruct megabase-sized human loci in YACsand to introduce them into the mouse germline provides a powerfulapproach to elucidating the functional components of very large orcrudely mapped loci as well as generating useful models of humandisease. Furthermore, the utilization of such technology forsubstitution of mouse loci with their human equivalents could provideunique insights into the expression and regulation of human geneproducts during development, their communication with other systems, andtheir involvement in disease induction and progression.

An important practical application of such a strategy is the“humanization” of the mouse humoral immune system. Introduction of humanimmunoglobulin (Ig) loci into mice in which the endogenous Ig genes havebeen inactivated offers the opportunity to study the mechanismsunderlying programmed expression and assembly of antibodies as well astheir role in B-cell development. Furthermore, such a strategy couldprovide an ideal source for production of fully human monoclonalantibodies (mAbs)—an important milestone towards fulfilling the promiseof antibody therapy in human disease. Fully human antibodies areexpected to minimize the immunogenic and allergic responses intrinsic tomouse or mouse-derivatized mAbs and thus to increase the efficacy andsafety of the administered antibodies. The use of fully human antibodiescan be expected to provide a substantial advantage in the treatment ofchronic and recurring human diseases, such as inflammation,autoimmunity, and cancer, which require repeated antibodyadministrations.

One approach towards this goal was to engineer mouse strains deficientin mouse antibody production with large fragments of the human Ig lociin anticipation that such mice would produce a large repertoire of humanantibodies in the absence of mouse antibodies. Large human Ig fragmentswould preserve the large variable gene diversity as well as the properregulation of antibody production and expression. By exploiting themouse machinery for antibody diversification and selection and the lackof immunological tolerance to human proteins, the reproduced humanantibody repertoire in these mouse strains should yield high affinityantibodies against any antigen of interest, including human antigens.Using the hybridoma technology, antigen-specific human mAbs with thedesired specificity could be readily produced and selected. This generalstrategy was demonstrated in connection with our generation of the firstXenoMouse mouse strains, as published in 1994. (See Green et al. NatureGenetics 7:13-21 (1994)) The XenoMouse strains were engineered withyeast artificial chromosomes (YACs) containing 245 kb and 190 kb-sizedgermline configuration fragments of the human heavy chain locus andkappa light chain locus, respectively, which contained core variable andconstant region sequences. Id. The human Ig containing YACs proved to becompatible with the mouse system for both rearrangement and expressionof antibodies and were capable of substituting for the inactivated mouseIg genes. This was demonstrated by their ability to induce B-celldevelopment, to produce an adult-like human repertoire of fully humanantibodies, and to generate antigen-specific human mAbs. These resultsalso suggested that introduction of larger portions of the human Ig locicontaining greater numbers of V genes, additional regulatory elements,and human Ig constant regions might recapitulate substantially the fullrepertoire that is characteristic of the human humoral response toinfection and immunization. The work of Green et al. was recentlyextended to the introduction of greater than approximately 80% of thehuman antibody repertoire through introduction of megabase sized,germline configuration YAC fragments of the human heavy chain loci andkappa light chain loci, respectively. See Mendez et al. Nature Genetics15:146-156 (1997) and U.S. patent application Ser. No. 08/759,620, filedDec. 3, 1996, the disclosures of which are hereby incorporated byreference.

The production of the XenoMouse mice is further discussed and delineatedin U.S. patent application Ser. No. 07/466,008, filed Jan. 12, 1990,Ser. No. 07/610,515, filed Nov. 8, 1990, Ser. No. 07/919,297, filed Jul.24, 1992, Ser. No. 07/922,649, filed Jul. 30, 1992, filed Ser. No.08/031,801, filed Mar. 15, 1993, Ser. No. 08/112,848, filed Aug. 27,1993, Ser. No. 08/234,145, filed Apr. 28, 1994, Ser. No. 08/376,279,filed Jan. 20, 1995, 08/430,938, Apr. 27, 1995, Ser. No. 08/464,584,filed Jun. 5, 1995, Ser. No. 08/464,582, filed Jun. 5, 1995, Ser. No.08/463,191, filed Jun. 5, 1995, Ser. No. 08/462,837, filed Jun. 5, 1995,Ser. No. 08/486,853, filed Jun. 5, 1995, Ser. No. 08/486,857, filed Jun.5, 1995, Ser. No. 08/486,859, filed Jun. 5, 1995, Ser. No. 08/462,513,filed Jun. 5, 1995, Ser. No. 08/724,752, filed Oct. 2, 1996, and Ser.No. 08/759,620, filed Dec. 3, 1996 and U.S. Pat. Nos. 6,162,963,6,150,584, 6,114,598, 6,075,181, and 5,939,598 and Japanese Patent Nos.3 068 180 B2, 3 068 506 B2, and 3 068 507 B2. See also Mendez et al.Nature Genetics 15:146-156 (1997) and Green and Jakobovits J. Exp. Med.188:483-495 (1998). See also European Patent No., EP 0 463 151 B1, grantpublished Jun. 12, 1996, International Patent Application No., WO94/02602, published Feb. 3, 1994, International Patent Application No.,WO 96/34096, published Oct. 31, 1996, WO 98/24893, published Jun. 11,1998, WO 00/76310, published Dec. 21, 2000, WO 03/47336. The disclosuresof each of the above-cited patents, applications, and references arehereby incorporated by reference in their entirety.

In an alternative approach, others, including GenPharm International,Inc., have utilized a “minilocus” approach. In the minilocus approach,an exogenous Ig locus is mimicked through the inclusion of pieces(individual genes) from the Ig locus. Thus, one or more V_(H) genes, oneor more D_(H) genes, one or more J_(H) genes, a mu constant region, anda second constant region (preferably a gamma constant region) are formedinto a construct for insertion into an animal. This approach isdescribed in U.S. Pat. No. 5,545,807 to Surani et al. and U.S. Pat. Nos.5,545,806, 5,625,825, 5,625,126, 5,633,425, 5,661,016, 5,770,429,5,789,650, 5,814,318, 5,877,397, 5,874,299, and 6,255,458 each toLonberg and Kay, U.S. Pat. Nos. 5,591,669 and 6,023,010 to Krimpenfortand Berns, U.S. Pat. Nos. 5,612,205, 5,721,367, and 5,789,215 to Bernset al., and U.S. Pat. No. 5,643,763 to Choi and Dunn, and GenPharmInternational U.S. patent application Ser. No. 07/574,748, filed Aug.29, 1990, Ser. No. 07/575,962, filed Aug. 31, 1990, Ser. No. 07/810,279,filed Dec. 17, 1991, Ser. No. 07/853,408, filed Mar. 18, 1992, Ser. No.07/904,068, filed Jun. 23, 1992, Ser. No. 07/990,860, filed Dec. 16,1992, Ser. No. 08/053,131, filed Apr. 26, 1993, Ser. No. 08/096,762,filed Jul. 22, 1993, Ser. No. 08/155,301, filed Nov. 18, 1993, Ser. No.08/161,739, filed Dec. 3, 1993, Ser. No. 08/165,699, filed Dec. 10,1993, Ser. No. 08/209,741, filed Mar. 9, 1994, the disclosures of whichare hereby incorporated by reference. See also European Patent No. 0 546073 B1, International Patent Application Nos. WO 92/03918, WO 92/22645,WO 92/22647, WO 92/22670, WO 93/12227, WO 94/00569, WO 94/25585, WO96/14436, WO 97/13852, and WO 98/24884 and U.S. Pat. No. 5,981,175, thedisclosures of which are hereby incorporated by reference in theirentirety. See further Taylor et al., 1992, Chen et al., 1993, Tuaillonet al., 1993, Choi et al., 1993, Lonberg et al., (1994), Taylor et al.,(1994), and Tuaillon et al., (1995), Fishwild et al., (1996), thedisclosures of which are hereby incorporated by reference in theirentirety.

Kirin has also demonstrated the generation of human antibodies from micein which, through microcell fusion, large pieces of chromosomes, orentire chromosomes, have been introduced. See European PatentApplication Nos. 773 288 and 843 961, the disclosures of which arehereby incorporated by reference. Xenerex Biosciences is developing atechnology for the potential generation of human antibodies. In thistechnology, SCID mice are reconstituted with human lymphatic cells,e.g., B and/or T cells. Mice are then immunized with an antigen and cangenerate an immune response against the antigen. See U.S. Pat. Nos.5,476,996, 5,698,767, and 5,958,765.

Human anti-mouse antibody (HAMA) responses have led the industry toprepare chimeric or otherwise humanized antibodies. While chimericantibodies have a human constant region and a murine variable region, itis expected that certain human anti-chimeric antibody (HACA) responseswill be observed, particularly in chronic or multi-dose utilizations ofthe antibody. Thus, it would be desirable to provide fully humanantibodies against EGFRvIII in order to vitiate concerns and/or effectsof HAMA or HACA response.

Antibody Therapeutics

As discussed herein, the function of the EGFRvIII antibody appearsimportant to at least a portion of its mode of operation. By function,it is meant, by way of example, the activity of the EGFRvIII antibody inoperation with EGFRvIII. Accordingly, in certain respects, it may bedesirable in connection with the generation of antibodies as therapeuticcandidates against EGFRvIII that the antibodies be capable of fixingcomplement and recruiting cytotoxic lymphocytes thus participating inCDC and ADCC. There are a number of isotypes of antibodies that arecapable of the same, including, without limitation, the following:murine IgM, murine IgG2a, murine IgG2b, murine IgG3, human IgM, humanIgG1, human IgG3, and human IgA. Also, it may be desirable in connectionwith the generation of antibodies as therapeutic candidates againstEGFRvIII that the antibodies be capable of activating antibody-dependentcelluclar cytotoxicity (ADCC), through engagement of Fc receptors oneffectors cells such as natural killer (NK) cells. There are a number ofisotypes of antibodies that are capable of ADCC, including, withoutlimitation, the following: murine IgG2a, murine IgG2b, murine IgG3,human IgG1, and human IgG3. It will be appreciated that antibodies thatare generated need not initially possess such an isotype but, rather,the antibody as generated can possess any isotype and the antibody canbe isotype switched thereafter using conventional techniques that arewell known in the art. Such techniques include the use of directrecombinant techniques (see e.g., U.S. Pat. No. 4,816,397) and cell-cellfusion techniques (see e.g., U.S. Pat. Nos. 5,916,771 and 6,207,418),among others.

In the cell-cell fusion technique, a myeloma or other cell line isprepared that possesses a heavy chain with any desired isotype andanother myeloma or other cell line is prepared that possesses the lightchain. Such cells can, thereafter, be fused and a cell line expressingan intact antibody can be isolated.

By way of example, certain anti-EGFRvIII antibodies discussed herein arehuman anti-EGFRvIII IgG1 antibodies. If such antibody possessed desiredbinding to the EGFRvIII molecule, it could be readily isotype switchedto generate a human IgM, human IgG3, or human IgGA while stillpossessing the same variable region (which defines the antibody'sspecificity and some of its affinity). Such molecules, including IgG1,would then be capable of fixing complement and participating in CDC,and, if comprising and IgG1 or IgG3 constant region, such moleculeswould also be capable of participating in antibody-dependent cellularcytotoxicity (ADCC) through recruiting cytotoxic lymphocytes.

Accordingly, as antibody candidates are generated that meet desired“structural” attributes as discussed above, they can generally beprovided with at least certain of the desired “functional” attributesthrough isotype switching.

Design and Generation of Other Therapeutics

Based on the activity of the antibodies that are produced andcharacterized herein with respect to EGFRvIII, the design of othertherapeutic modalities beyond antibody moieties is facilitated. Suchmodalities include, without limitation, advanced antibody therapeutics,such as bispecific antibodies, immunotoxins, and radiolabeledtherapeutics, generation of peptide therapeutics, gene therapies,particularly intrabodies, antisense therapeutics, and small molecules.

In connection with the generation of advanced antibody therapeutics,where complement fixation and recruitment of cytoxic lymphocytes is adesirable attribute, it is possible to enhance cell killing through theuse of bispecifics, immunotoxins, or radiolabels, for example.

For example, in connection with bispecific antibodies, bispecificantibodies can be generated that comprise (i) two antibodies one with aspecificity to EGFRvIII and another to a second molecule that areconjugated together, (ii) a single antibody that has one chain specificto EGFRvIII and a second chain specific to a second molecule, or (iii) asingle chain antibody that has specificity to EGFRvIII and the othermolecule. Such bispecific antibodies can be generated using techniquesthat are well known for example, in connection with (i) and (ii) seee.g., Fanger et al. Immunol Methods 4:72-81 (1994) and Wright andHarris, supra. and in connection with (iii) see e.g., Traunecker et al.Int. J. Cancer (Suppl.) 7:51-52 (1992). In each case, the secondspecificity can be made to the Fc chain activation receptors, including,without limitation, CD16 or CD64 (see e.g., Deo et al. 18:127 (1997))CD3 (Micromet's BiTE technology) or CD89 (see e.g., Valerius et al.Blood 90:4485-4492 (1997)). Bispecific antibodies prepared in accordancewith the foregoing would be likely to kill cells expressing EGFRvIII,and particularly those cells in which the EGFRvIII antibodies of theinvention are effective.

In connection with immunotoxins, antibodies can be modified to act asimmunotoxins utilizing techniques that are well known in the art. Seee.g., Vitetta Immunol Today 14:252 (1993). See also U.S. Pat. No.5,194,594. In connection with the preparation of radiolabeledantibodies, such modified antibodies can also be readily preparedutilizing techniques that are well known in the art. See e.g., Junghanset al. in Cancer Chemotherapy and Biotherapy 655-686 (2d edition,Chafner and Longo, eds., Lippincott Raven (1996)). See also U.S. Pat.Nos. 4,681,581, 4,735,210, 5,101,827, 5,102,990 (RE 35,500), 5,648,471,and 5,697,902. Each of immunotoxins and radiolabeled molecules would belikely to kill cells expressing EGFRvIII, and particularly those cellsin which the antibodies described herein are effective.

The antibodies can be designed to bind more quickly, or to dissociatemore slowly from the epitope, and thus the antibodies themselves can bedesigned therapeutics. The altered characterisitics of the antibodiescan be used, for example, in the administration of a therapeutic to apatient.

Therapeutic Immunoconjugates

As will be appreciated, antibodies conjugated to drugs, toxins, or othermolecules (immunoconjugates or immunotoxins) are highly useful in thetargeted killing of cells that express a molecule that can bespecifically bound by a specific binding molecule, such as an antibody.As discussed above, EGFRvIII is not known to be expressed on any normaltissues. Further, EGFRvIII shows significant expression in numeroushuman tumors. Accordingly, EGFRvIII is a highly attractive molecule fortargeting with an immunotoxin.

Many reports have appeared on the attempted specific targeting of tumorcells with monoclonal antibody-drug conjugates (Sela et al. inImmunoconjugates 189-216 (C. Vogel, ed. 1987); Ghose et al, in TargetedDrugs 1-22 (E. Goldberg, ed. 1983); Diener et al, in Antibody MediatedDelivery Systems 1-23 (J. Rodwell, ed. 1988); Pietersz et al, inAntibody Mediated Delivery Systems 25-53 (J. Rodwell, ed. 1988); Bumolet al, in Antibody Mediated Delivery Systems 55-79 (J. Rodwell, ed.1988). Cytotoxic drugs such as methotrexate, daunorubicin, doxorubicin,vincristine, vinblastine, melphalan, mitomycin C, and chlorambucil havebeen conjugated to a variety of murine monoclonal antibodies. In somecases, the drug molecules were linked to the antibody molecules throughan intermediary carrier molecule such as serum albumin (Garnett et al.Cancer Res. 46:2407-2412 (1986); Ohkawa et al. Cancer Immumol.Immunother. 23:81-86 (1986); Endo et al. Cancer Res. 47:1076-1080(1980)), dextran (Hurwitz et al. Appl. Biochem. 2:25-35 (1980); Manabiet al. Biochem. Pharmacol. 34:289-291 (1985); Dillman et al. Cancer Res.46:4886-4891 (1986); Shoval et al. Proc. Natl. Acad. Sci. 85: 8276-8280(1988)), or polyglutamic acid (Tsukada et al. J. Natl. Canc. Inst.73:721-729 (1984); Kato et al. J. Med. Chem. 27:1602-1607 (1984);Tsukada et al. Br. J. Cancer 52:111-116 (1985)).

A wide array of linker technologies has been employed for thepreparation of such immunoconjugates and both cleavable andnon-cleavable linkers have been investigated. In most cases, the fullcytotoxic potential of the drugs could only be observed, however, if thedrug molecules could be released from the conjugates in unmodified format the target site.

One of the cleavable linkers that has been employed for the preparationof antibody-drug conjugates is an acid-labile linker based oncis-aconitic acid that takes advantage of the acidic environment ofdifferent intracellular compartments such as the endosomes encounteredduring receptor mediated endocytosis and the lysosomes. Shen and Ryserintroduced this method for the preparation of conjugates of daunorubicinwith macromolecular carriers (Biochem. Biophys. Res. Commun.102:1048-1054 (1981)). Yang and Reisfeld used the same technique toconjugate daunorubicin to an anti-melanoma antibody (J. Natl. Canc.Inst. 80:1154-1159 (1988)). Recently, Dillman et al. also used anacid-labile linker in a similar fashion to prepare conjugates ofdaunorubicin with an anti-T cell antibody (Cancer Res. 48:6097-6102(1988)).

An alternative approach, explored by Trouet et al. involved linkingdaunorubicin to an antibody via a peptide spacer arm (Proc. Natl. Acad.Sci. 79:626-629 (1982)). This was done under the premise that free drugcould be released from such a conjugate by the action of lysosomalpeptidases.

In vitro cytotoxicity tests, however, have revealed that antibody-drugconjugates rarely achieved the same cytotoxic potency as the freeunconjugated drugs. This suggested that mechanisms by which drugmolecules are released from the antibodies are very inefficient. In thearea of immunotoxins, conjugates formed via disulfide bridges betweenmonoclonal antibodies and catalytically active protein toxins were shownto be more cytotoxic than conjugates containing other linkers. See,Lambert et al. J. Biol. Chem. 260:12035-12041 (1985); Lambert et al. inImmunotoxins 175-209 (A. Frankel, ed. 1988); Ghetie et al. Cancer Res.48:2610-2617 (1988). This was attributed to the high intracellularconcentration of glutathione contributing to the efficient cleavage ofthe disulfide bond between an antibody molecule and a toxin. Despitethis, there are only a few reported examples of the use of disulfidebridges for the preparation of conjugates between drugs andmacromolecules. Shen et al. described the conversion of methotrexateinto a mercaptoethylamide derivative followed by conjugation withpoly-D-lysine via a disulfide bond (J. Biol. Chem. 260:10905-10908(1985)). In addition, a report described the preparation of a conjugateof the trisulfide-containing toxic drug calicheamycin with an antibody(Menendez et al. Fourth International Conference on Monoclonal AntibodyImmunoconjugates for Cancer, San Diego, Abstract 81 (1989)). Anotherreport described the preparation of a conjugate of thetrisulfide-containing toxic drug calicheamycin with an antibody (Hinmanet al, 53 Cancer Res. 3336-3342 (1993)).

One reason for the lack of disulfide linked antibody-drug conjugates isthe unavailability of cytotoxic drugs that bear a sulfur atom containingmoiety that can be readily used to link the drug to an antibody via adisulfide bridge. Furthermore, chemical modification of existing drugsis difficult without diminishing their cytotoxic potential.

Another major drawback with existing antibody-drug conjugates is theirinability to deliver a sufficient concentration of drug to the targetsite because of the limited number of targeted antigens and therelatively moderate cytotoxicity of cancerostatic drugs likemethotrexate, daunorubicin and vincristine. In order to achievesignificant cytotoxicity, linkage of a large number of drug moleculeseither directly to the antibody or through a polymeric carrier moleculebecomes necessary. However such heavily modified antibodies oftendisplay impaired binding to the target antigen and fast in vivoclearance from the blood stream.

Maytansinoids are highly cytotoxic drugs. Maytansine was first isolatedby Kupchan et al. from the east African shrub Maytenus serrata and shownto be 100 to 1000 fold more cytotoxic than conventional cancerchemotherapeutic agents like methotrexate, daunorubicin, and vincristine(U.S. Pat. No. 3,896,111). Subsequently, it was discovered that somemicrobes also produce maytansinoids, such as maytansinol and C-3 estersof maytansinol (U.S. Pat. No. 4,151,042). Synthetic C-3 esters ofmaytansinol and analogues of maytansinol have also been reported(Kupchan et al. J. Med. Chem. 21:31-37 (1978); Higashide et al. Nature270:721-722 (1977); Kawai et al. Chem. Pharm. Bull. 32:3441-3451(1984)). Examples of analogues of maytansinol from which C-3 esters havebeen prepared include maytansinol with modifications on the aromaticring (e.g. dechloro) or at the C-9, C-14 (e.g. hydroxylated methylgroup), C-15, C-18, C-20 and C-4,5.

The naturally occurring and synthetic C-3 esters can be classified intotwo groups:

-   -   (a) C-3 esters with simple carboxylic acids (U.S. Pat. Nos.        4,248,870; 4,265,814; 4,308,268; 4,308,269; 4,309,428;        4,317,821; 4,322,348; and 4,331,598), and    -   (b) C-3 esters with derivatives of N-methyl-L-alanine (U.S. Pat.        Nos. 4,137,230; 4,260,608; 5,208,020; and Chem. Pharm. Bull.        12:3441 (1984)).

Esters of group (b) were found to be much more cytotoxic than esters ofgroup (a).

Maytansine is a mitotic inhibitor. Treatment of L1210 cells in vivo withmaytansine has been reported to result in 67% of the cells accumulatingin mitosis. Untreated control cells were reported to demonstrate amitotic index ranging from between 3.2 to 5.8% (Sieber et al. 43Comparative Leukemia Research 1975, Bibl. Haemat. 495-500 (1976)).Experiments with sea urchin eggs and clam eggs have suggested thatmaytansine inhibits mitosis by interfering with the formation ofmicrotubules through the inhibition of the polymerization of themicrotubule protein, tubulin (Remillard et al. Science 189:1002-1005(1975)).

In vitro, P388, L1210, and LY5178 murine leukemic cell suspensions havebeen found to be inhibited by maytansine at doses of 10⁻³ to10⁻¹.mu.g/.mu.l with the P388 line being the most sensitive. Maytansinehas also been shown to be an active inhibitor of in vitro growth ofhuman nasopharyngeal carcinoma cells, and the human acute lymphoblasticleukemia line CEM was reported inhibited by concentrations as low as10⁻⁷ mg/ml (Wolpert-DeFillippes et al. Biochem. Pharmacol. 24:1735-1738(1975)).

In vivo, maytansine has also been shown to be active. Tumor growth inthe P388 lymphocytic leukemia system was shown to be inhibited over a50- to 100-fold dosage range which suggested a high therapeutic index;also significant inhibitory activity could be demonstrated with theL1210 mouse leukemia system, the human Lewis lung carcinoma system andthe human B-16 melanocarcinoma system (Kupchan, Ped. Proc. 33:2288-2295(1974)).

Current methods of conjugation of maytansinoids with cell binding agents(such as antibodies) involve two reaction steps. A cell binding agent,for example an antibody, is first modified with a cross-linking reagentsuch as N-succinimidyl pyridyldithiopropionate (SPDP) to introducedithiopyridyl groups into the antibody (Carlsson et al. Biochem. J.173:723-737 (1978); U.S. Pat. No. 5,208,020). In a second step, areactive maytansinoid having a thiol group, such as DM1 (formally termedN^(2′)-deacetyl-N^(2′)-(3-mercapto-1-oxopropyl)-maytansine, as thestarting reagent., is added to the modified antibody, resulting in thedisplacement of the thiopyridyl groups in the modified antibodies, andthe production of disulfide-linked cytotoxic maytansinoid/antibodyconjugates (U.S. Pat. No. 5,208,020). A one-step process for conjugationof maytansinoids is described in U.S. Pat. No. 6,441,163.Maytansinoid-based immunotoxin technology is available from ImmunogenCorporation (Cambridge, Mass.).

Another important toxin technology is based upon auristatin toxins.Auristatins are derived from Dolastatin 10 that was obtained from theIndian Ocean sea hare Dolabella, as a potent cell growth inhibitorysubstance. See U.S. Pat. Nos. 4,816,444 and 4,978,744. With respect toother Dolastatins, see also U.S. Pat. No. 4,414,205 (Dolastatin-1, 2,and 3), U.S. Pat. No. 5,076,973 (Dolastatin-3), U.S. Pat. No. 4,486,414(Dolastatin-A and B); U.S. Pat. No. 4,986,988 (Dolastatin-13), U.S. Pat.No. 5,138,036 (Dolastatin-14), and U.S. Pat. No. 4,879,278(dolastatin-15). Isolated and synthesized by Dr. Pettit and colleaguesat the University of Arizona, a variety of auristatine derivatives havebeen tested and shown to be highly toxic to cells. See Pettit et al.Antineoplastic agents 337. Synthesis of dolastatin 10 structuralmodifications. Anticancer Drug Des. 10(7):529-44 (1995), Woyke et al. Invitro activities and postantifungal effects of the potent dolastatin 10structural modification auristatin PHE. Antimicrobial Agents andChemotherapy. 45:3580-3584 (2001), Pettit et al. Specific activities ofdolastatin 10 and peptide derivatives against Cryptococcus neoformans.Antimicrobial Agents and Chemotherapy. 42:2961-2965 (1998),WoykeThree-dimensional visualization of microtubules during theCryptococcus neoformans cell cycle and the effects of auristatin PHE onmicrotubule integrity and nuclear localization. Submitted, AntimicrobialAgents and Chemotherapy.

Recently, additional auristatin derivatives have been developed thatappear quite effective when delivered as payloads on antibodies. Forexample monomethyl auristatin E (MMAE) has been shown as a potent toxinfor tumor cells when conjugated to tumor specific antibodies. Doroninaet al. Development of potent monoclonal antibody auristatin conjugatesfor cancer therapy. Nature Biotechnology. (2003) (available online),Francisco et al. cAC10-veMMAE, an anti-CD30-monomethyl auristatin Econjugate with potent and selective antitumor activity. Blood. (2003)May 8 [Epub ahead of print]. Epub 2003 Apr. 24 (available online). Inaddition to the toxicity of the auristatin molecule, research has shownthat peptide-linked conjugates are more stable, and, thus, more specificand less toxic to normal tissues than other linker technologies inbuffers and plasma. Doronina et al. Development of potent monoclonalantibody auristatin conjugates for cancer therapy. Nature Biotechnology.(2003) (available online), Francisco et al. cAC10-veMMAE, ananti-CD30-monomethyl auristatin E conjugate with potent and selectiveantitumor activity. Blood. (2003) May 8 [Epub ahead of print]. Epub 2003Apr. 24 (available online). Such linkers are based on a branched peptidedesign and include, for example, mAb-valine-citrulline-MMAE andmAb-phenylalanine-lysine-MMAE conjugates. Doronina et al. Development ofpotent monoclonal antibody auristatin conjugates for cancer therapy.Nature Biotechnology. (2003) (available online), Francisco et al.cAC10-veMMAE, an anti-CD30-monomethyl auristatin E conjugate with potentand selective antitumor activity. Blood. (2003) May 8 [Epub ahead ofprint]. Epub 2003 Apr. 24 (available online). Such designs andconjugation techniques are described, for example, by King et al.Monoclonal antibody conjugates of doxorubicin prepared with branchedpeptide linkers: inhibition of aggregation by methoxytriethyleneglycolchains. J Med Chem. 45(19):4336-43 (2002) and Dubowchik et al. CathepsinB-sensitive dipeptide prodrugs. 2. Models of anticancer drugs paclitaxel(Taxol), mitomycin C and doxorubicin. Bioorg Med Chem Lett.8(23):3347-52 (1998). Auristatin E-based immunotoxin technology basedupon the foregoing is available from Seattle Genetics Corporation(Seattle, Wash.).

There are a large number of novel microtubule effecting compoundsobtained from natural sources-extracts, and semisynthetic and syntheticanalogs that appear to possess potential as toxins for the generation ofimmunoconjugates. (see the website at newmedinc “dot” com). Suchmolecules and examples of drug products utilizing them, include thefollowing: Colchicine-site Binders (Curacin), Combretastatins (AVE806,Combretastatin A-4 prodrug (CA4P), Oxi-4503), Cryptophycins (LY355703),Discodermolide, Dolastatin and Analogs (Auristatin PHE, Dolastatin 10,ILX-651, Symplostatin 1, TZT-1027), Epothilones (BMS-247550, BMS-310705,EP0906, KOS-862, ZK-EPO), Eleutherobin, FR182877, Halichondrin B(E7389), Halimide (NPI-2352 and NPI-2358), Hemiasterlins (HTI-286),Laulimalide, Maytansinoids (“DM1”)(Bivatuzumab mertansine, Cantuzumabmertansine, huN901-DM1/BB-10901 TAP, MLN591DM1, My9-6-DM1,Trastuzumab-DM1), PC-SPES, Peloruside A, Resveratrol,S-allylmercaptocysteine (SAMC), Spongistatins, Vitilevuamide, MolecularMotor-Kinesins (SB-715992), Designed Colchicine-Site Binders (A-289099,A-293620/A-318315, ABT-751/E7010, D-24851/D-64131, ZD6126), Other NovelSpindle Poisons (2-Methoxyestradiol (2-ME2), Bezimidazole Carbamates(ANG 600 series, Mebendazole), CP248/CP461, HMN-214, R440, SDX-103,T67/T607). Further, additional marine derived toxins are reviewed inMayer, A. M. S. Marine Pharmacology in 1998: Antitumor and CytotoxicCompounds. The Pharmacologist. 41(4):159-164 (1999).

Therapeutic Administration and Formulations

A prolonged duration of action will allow for less frequent and moreconvenient dosing schedules by alternate parenteral routes such asintravenous, subcutaneous or intramuscular injection.

When used for in vivo administration, antibody formulations describedherein should be sterile. This is readily accomplished, for example, byfiltration through sterile filtration membranes, prior to or followinglyophilization and reconstitution. Antibodies ordinarily will be storedin lyophilized form or in solution. Therapeutic antibody compositionsgenerally are placed into a container having a sterile access port, forexample, an intravenous solution bag or vial having an adapter thatallows retrieval of the formulation, such as a stopper pierceable by ahypodermic injection needle.

The route of antibody administration is in accord with known methods,e.g., injection or infusion by intravenous, intraperitoneal,intracerebral, intramuscular, intraocular, intraarterial, intrathecal,inhalation or intralesional routes, or by sustained release systems asnoted below. Antibodies are preferably administered continuously byinfusion or by bolus injection.

An effective amount of antibody to be employed therapeutically willdepend, for example, upon the therapeutic objectives, the route ofadministration, and the condition of the patient. Accordingly, it ispreferred for the therapist to titer the dosage and modify the route ofadministration as required to obtain the optimal therapeutic effect.Typically, the clinician will administer antibody until a dosage isreached that achieves the desired effect. The progress of this therapyis easily monitored by conventional assays or by the assays describedherein.

Antibodies as described herein can be prepared in a mixture with apharmaceutically acceptable carrier. Therapeutic compositions can beadministered intravenously or through the nose or lung, preferably as aliquid or powder aerosol (lyophilized). Composition can also beadministered parenterally or subcutaneously as desired. Whenadministered systemically, therapeutic compositions should be sterile,pyrogen-free and in a parenterally acceptable solution having due regardfor pH, isotonicity, and stability. These conditions are known to thoseskilled in the art. Briefly, dosage formulations of the compounds areprepared for storage or administration by mixing the compound having thedesired degree of purity with physiologically acceptable carriers,excipients, or stabilizers. Such materials are non-toxic to therecipients at the dosages and concentrations employed, and includebuffers such as TRIS HCl, phosphate, citrate, acetate and other organicacid salts; antioxidants such as ascorbic acid; low molecular weight(less than about ten residues) peptides such as polyarginine, proteins,such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymerssuch as polyvinylpyrrolidinone; amino acids such as glycine, glutamicacid, aspartic acid, or arginine; monosaccharides, disaccharides, andother carbohydrates including cellulose or its derivatives, glucose,mannose, or dextrins; chelating agents such as EDTA; sugar alcohols suchas mannitol or sorbitol; counterions such as sodium and/or nonionicsurfactants such as TWEEN, PLURONICS or polyethyleneglycol.

Sterile compositions for injection can be formulated according toconventional pharmaceutical practice as described in Remington'sPharmaceutical Sciences (18^(th) ed, Mack Publishing Company, Easton,Pa., 1990). For example, dissolution or suspension of the activecompound in a vehicle such as water or naturally occurring vegetable oillike sesame, peanut, or cottonseed oil or a synthetic fatty vehicle likeethyl oleate or the like may be desired. Buffers, preservatives,antioxidants and the like can be incorporated according to acceptedpharmaceutical practice.

Suitable examples of sustained-release preparations includesemipermeable matrices of solid hydrophobic polymers containing thepolypeptide, which matrices are in the form of shaped articles, films ormicrocapsules. Examples of sustained-release matrices includepolyesters, hydrogels (e.g., poly(2-hydroxyethyl-methacrylate) asdescribed by Langer et al., J. Biomed Mater. Res., (1981) 15:167-277 andLanger, Chein. Tech., (1982) 12:98-105, or poly(vinylalcohol)),polylactides (U.S. Pat. No. 3,773,919, EP 58,481), copolymers ofL-glutamic acid and gamma ethyl-L-glutamate (Sidman et al., Biopolymers,(1983) 22:547-556), non-degradable ethylene-vinyl acetate (Langer etal., supra), degradable lactic acid-glycolic acid copolymers such as theLUPRON Depot™ (injectable microspheres composed of lactic acid-glycolicacid copolymer and leuprolide acetate), and poly-D-(−)-3-hydroxybutyricacid (EP 133,988).

While polymers such as ethylene-vinyl acetate and lactic acid-glycolicacid enable release of molecules for over 100 days, certain hydrogelsrelease proteins for shorter time periods. When encapsulated proteinsremain in the body for a long time, they may denature or aggregate as aresult of exposure to moisture at 37° C., resulting in a loss ofbiological activity and possible changes in immunogenicity. Rationalstrategies can be devised for protein stabilization depending on themechanism involved. For example, if the aggregation mechanism isdiscovered to be intermolecular S—S bond formation through disulfideinterchange, stabilization may be achieved by modifying sulfhydrylresidues, lyophilizing from acidic solutions, controlling moisturecontent, using appropriate additives, and developing specific polymermatrix compositions.

Sustained-released compositions also include preparations of crystals ofthe antibody suspended in suitable formulations capable of maintainingcrystals in suspension. These preparations when injected subcutaneouslyor intraperitoneally can produce a sustain release effect. Othercompositions also include liposomally entrapped antibodies. Liposomescontaining such antibodies are prepared by methods known per se: U.S.Pat. No. DE 3,218,121; Epstein et al., Proc. Natl. Acad. Sci. USA,(1985) 82:3688-3692; Hwang et al., Proc. Natl. Acad. Sci. USA, (1980)77:4030-4034; EP 52,322; EP 36,676; EP 88,046; EP 143,949; 142,641;Japanese patent application 83-118008; U.S. Pat. Nos. 4,485,045 and4,544,545; and EP 102,324.

The dosage of the antibody formulation for a given patient will bedetermined by the attending physician taking into consideration variousfactors known to modify the action of drugs including severity and typeof disease, body weight, sex, diet, time and route of administration,other medications and other relevant clinical factors. Therapeuticallyeffective dosages may be determined by either in vitro or in vivomethods.

An effective amount of the antibody to be employed therapeutically willdepend, for example, upon the therapeutic objectives, the route ofadministration, and the condition of the patient. Accordingly, it ispreferred that the therapist titer the dosage and modify the route ofadministration as required to obtain the optimal therapeutic effect. Atypical daily dosage might range from about 0.001 mg/kg to up to 100mg/kg or more, depending on the factors mentioned above. Typically, theclinician will administer the therapeutic antibody until a dosage isreached that achieves the desired effect. The progress of this therapyis easily monitored by conventional assays or as described herein.

It will be appreciated that administration of therapeutic entities inaccordance with the compositions and methods herein will be administeredwith suitable carriers, excipients, and other agents that areincorporated into formulations to provide improved transfer, delivery,tolerance, and the like. A multitude of appropriate formulations can befound in the formulary known to all pharmaceutical chemists: Remington'sPharmaceutical Sciences (18^(th) ed, Mack Publishing Company, Easton,Pa. (1990)), particularly Chapter 87 by Block, Lawrence, therein. Theseformulations include, for example, powders, pastes, ointments, jellies,waxes, oils, lipids, lipid (cationic or anionic) containing vesicles(such as Lipofectin™), DNA conjugates, anhydrous absorption pastes,oil-in-water and water-in-oil emulsions, emulsions carbowax(polyethylene glycols of various molecular weights), semi-solid gels,and semi-solid mixtures containing carbowax. Any of the foregoingmixtures may be appropriate in treatments and therapies in accordancewith the present invention, provided that the active ingredient in theformulation is not inactivated by the formulation and the formulation isphysiologically compatible and tolerable with the route ofadministration. See also Baldrick P. “Pharmaceutical excipientdevelopment: the need for preclinical guidance.” Regul. Toxicol.Pharmacol. 32(2):210-8 (2000), Wang W. “Lyophilization and developmentof solid protein pharmaceuticals.” Int. J. Pharm. 203(1-2):1-60 (2000),Charman WN “Lipids, lipophilic drugs, and oral drug delivery-someemerging concepts.” J Pharm Sci 0.89(8):967-78 (2000), Powell et al.“Compendium of excipients for parenteral formulations” PDA J Pharm SciTechnol. 52:238-311 (1998) and the citations therein for additionalinformation related to formulations, excipients and carriers well knownto pharmaceutical chemists.

Preparation of Antibodies

Antibodies, as described herein, were prepared through the utilizationof the XenoMouse® technology, as described below. Such mice, then, arecapable of producing human immunoglobulin molecules and antibodies andare deficient in the production of murine immunoglobulin molecules andantibodies. Technologies utilized for achieving the same are disclosedin the patents, applications, and references disclosed herein. Inparticular, however, a one embodiment of transgenic production of miceand antibodies therefrom is disclosed in U.S. patent application Ser.No. 08/759,620, filed Dec. 3, 1996 and International Patent ApplicationNos. WO 98/24893, published Jun. 11, 1998 and WO 00/76310, publishedDec. 21, 2000, the disclosures of which are hereby incorporated byreference. See also Mendez et al. Nature Genetics 15:146-156 (1997), thedisclosure of which is hereby incorporated by reference.

Through use of such technology, fully human monoclonal antibodies to avariety of antigens can be produced. In one embodiement, XenoMouse®lines of mice are immunized with an antigen of interest (e.g. EGFRvIII),lymphatic cells are recovered (such as B-cells) from the mice thatexpressed antibodies, and such cells are fused with a myeloid-type cellline to prepare immortal hybridoma cell lines, and such hybridoma celllines are screened and selected to identify hybridoma cell lines thatproduce antibodies specific to the antigen of interest. Provided hereinare methods for the production of multiple hybridoma cell lines thatproduce antibodies specific to EGFRvIII. Further, provided herein arecharacterization of the antibodies produced by such cell lines,including nucleotide and amino acid sequences of the heavy and lightchains of such antibodies.

Alternatively, instead of being fused to myeloma cells to generatehybridomas, the antibody produced by recovered cells, isolated fromimmunized XenoMouse® lines of mice, are screened further for reactivityagainst the initial antigen, preferably EGFRvIII protein. Such screeningincludes ELISA with EGFRvIII protein, in vitro binding to NR6 M cellsstably expressing full length EGFRvIII and internalization of EGFRvIIIreceptor by the antibodies in NR6 M cells. Single B cells secretingantibodies of interest are then isolated using a EGFRvIII-specifichemolytic plaque assay (Babcook et al., Proc. Natl. Acad. Sci. USA,i93:7843-7848 (1996)). Cells targeted for lysis are preferably sheep redblood cells (SRBCs) coated with the EGFRvIII antigen. In the presence ofa B cell culture secreting the immunoglobulin of interest andcomplement, the formation of a plaque indicates specificEGFRvIII-mediated lysis of the target cells. The single antigen-specificplasma cell in the center of the plaque can be isolated and the geneticinformation that encodes the specificity of the antibody is isolatedfrom the single plasma cell. Using reverse-transcriptase PCR, the DNAencoding the variable region of the antibody secreted can be cloned.Such cloned DNA can then be further inserted into a suitable expressionvector, preferably a vector cassette such as a pcDNA, more preferablysuch a pcDNA vector containing the constant domains of immunglobulinheavy and light chain. The generated vector can then be transfected intohost cells, preferably CHO cells, and cultured in conventional nutrientmedia modified as appropriate for inducing promoters, selectingtransformants, or amplifying the genes encoding the desired sequences.Herein, we describe the isolation of multiple single plasma cells thatproduce antibodies specific to EGFRvIII. Further, the genetic materialthat encodes the specificity of the anti-EGFRvIII antibody is isolated,introduced into a suitable expression vector that is then transfectedinto host cells.

B cells from XenoMouse mice may be also be used as a source of geneticmaterial from which antibody display libraries may be generated. Suchlibraries may be made in bacteriophage, yeast or in vitro via ribosomedisplay using ordinary skills in the art. Hyperimmunized XenoMouse micemay be a rich source from which high-affinity, antigen-reactiveantibodies may be isolated. Accordingly, XenoMouse mice hyperimmunizedagainst EGFRvIII may be used to generate antibody display libraries fromwhich high-affinity antibodies against EGFRvIII may be isolated. Suchlibraries could be screened against the pep3 oligopeptide and theresultingly derived antibodies screening against cells expressingEGFRvIII to confirm specificity for the natively display antigen. FullIgG antibody may then be expressed using recombinant DNA technology. Seee.g., WO 99/53049.

In general, antibodies produced by the above-mentioned cell linespossessed fully human IgG1 or IgG2 heavy chains with human kappa lightchains. In one embodiment, the antibodies possessed high affinities,typically possessing Kd's of from about 10⁻⁹ through about 10⁻¹³ M, whenmeasured by either solid phase and solution phase. In other embodimentsthe antibodies possessed lower affinities, from about 10⁻⁶ through about10⁻⁸ M.

As appreciated by one of skill in the art, antibodies in accordance withthe present embodiments can be expressed in cell lines other thanhybridoma cell lines. Sequences encoding particular antibodies can beused for transformation of a suitable mammalian host cell.Transformation can be by any known method for introducingpolynucleotides into a host cell, including, for example packaging thepolynucleotide in a virus (or into a viral vector) and transducing ahost cell with the virus (or vector) or by transfection procedures knownin the art, as exemplified by U.S. Pat. Nos. 4,399,216, 4,912,040,4,740,461, and 4,959; 455 (which patents are hereby incorporated hereinby reference). The transformation procedure used depends upon the hostto be transformed. Methods for introduction of heterologouspolynucleotides into mammalian cells are well known in the art andinclude dextran-mediated transfection, calcium phosphate precipitation,polybrene mediated transfection, protoplast fusion, electroporation,encapsulation of the polynucleotide(s) in liposomes, and directmicroinjection of the DNA into nuclei.

Mammalian cell lines available as hosts for expression are well known inthe art and include many immortalized cell lines available from theAmerican Type Culture Collection (ATCC), including but not limited toChinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK)cells, monkey kidney cells (COS), human hepatocellular carcinoma cells(e.g., Hep G2), and a number of other cell lines. Cell lines ofparticular preference are selected through determining which cell lineshave high expression levels and produce antibodies with constitutiveEGFRvIII binding properties.

EXAMPLES

The following examples, including the experiments conducted and theresults achieved are provided for illustrative purposes only and are notto be construed as limiting upon the present invention.

The strategy for generating EGFRvIII-specific antibodies initiallyinvolved immunization of XenoMouse mice with combinations of antigens(peptide, various soluble proteins, antigen-expressing cells) followedby isolation of antibody producing cells, either as through fusions toproduce hybridomas or isolation of B cell cells through theXenoMax™/SLAM™ technology. Antibody producing cells were subjected to aprimary screen for specificity by ELISA and a secondary screen for cellsurface binding by FMAT and/or FACS. Internalization assays were thenconducted to identify antibodies that would be useful for drug delivery.Affinities of the antibodies were measured. Certain antibodies wereselected for epitope mapping. In addition, certain antibodies wereselected for in vitro and in vivo tests to analyze the efficacy of suchantibodies for treatment of cancers.

Example 1 Antigen Preparation

A. EGFRvIII PEP3-KLH Antigen Preparation

In connection with Example 2, the 14-mer human EGFRvIII PEP3 (L E E K KG N Y V V T D H C (SEQ ID NO: 56)) peptide was custom synthesized by R&DSystems. The PEP3 peptide was then conjugated to keyhole limpethemocyanin (KLH), as follows: EGFRvIII PEP3 (200 mcg) (R&D) was mixedwith 50 mcg of keyhole limpet hemocyanin (KLH; Pierce, Rockford, Ill.)to a final volume of 165 mcl using distilled water. 250 mcl ofconjugation buffer (0.1M MES, 0.9M NaCl, pH 4.7) was added and EGFRvIIIPEP3 and KLH were crosslinked by the addition of 25 mcl of 10 mg/mlstock solution of 1-ethyl-3-[3-dimethylaminopropyl]carbodiimidehydrochloride (EDC, Pierce, Rockford, Ill.). Conjugate was incubated for2 hours at room temperature and the unreacted EDC was removed bycentrifugation through a 1 kDa filter (Centrifugal filter; Millipore,Bedford, Mass.) using PBS pH 7.4.

In connection with Example 3, the 14-mer human EGFRvIII PEP3 (L E E KK GN Y V V T D H C (SEQ ID NO: 56)) peptide was custom synthesized. ThePEP3 peptide was then conjugated to KLH, as follows: human EGFRvIII PEP3(200 mcg) was mixed with 50 mcg of keyhole limpet hemocyanin (KLH;Pierce, Rockford, Ill.) to a final volume of 165 mcl using distilledwater. 250 mcl of conjugation buffer (0.1M MES, 0.9M NaCl, pH 4.7) wasadded and EGFRvIII PEP3 and KLH were crosslinked by the addition of 25mcl of 10 mg/ml stock solution of1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC,Pierce, Rockford, Ill.). Conjugate was incubated for 2 hours at roomtemperature and the unreacted EDC was removed by centrifugation througha 1 kDa filter (Centrifugal filter; Millipore, Bedford, Mass.) using PBSpH 7.4.

B. B300.19/EGFRvIII Transfectants

In order to prepare the B300.19/EGFRvIII transfectants, wild type EGFRwas initially cloned from A431 cells and EGFR gene was modified to codefor EGFRvIII to delete the codons encoding residues 6-273, with a codonencoding a Glycine residue created at the junction of the deletion. Thedeletion occurs within the codons surrounding the deletion GTT (Valine)and CGT (Arginine), such that the resulting codon after the deletion isGGT (Glycine). (Wikstrand et al. J Neurovirol. 4(2):148-58 (1998)) 1.Cloning of wild type EGFR Construct:

PolyA+mRNA was extracted from A431 (ATCC) cells usingMicro-fast RNA kit(Invitrogen, Burlington, ON). Total cDNA was synthesized from polyA+mRNAwith random pdN6 primers and M-MuLV reverse transcriptase (NEB, NewEngland Biolabs, Beverly, Mass.). A 2.3 kb PCR product was amplifiedfrom A431 cDNA with the following primers:

sense (SEQ ID NO: 62) 5′-GGATCTCGAGCCAGACCGGAACGACAGGCCACCTC-3′;anti-sense (SEQ ID NO: 63) 5′-CGGATCTCGAGCCGGAGCCCAGCACTTTGATCTT-3′

using Pfu DNA polymerase.

The PCR product was digested with XhoI, gel purified and ligated intoplasmid pWBFNP (see International Patent Application No. WO 99/45031,the disclosure of which is hereby incorporated by reference) linearizedwith XhoI to yield plasmid Wt-EGFR/pWBFNP.

2. Generation of EGFRvIII Construct:

PCR products amplified from plasmid Wt-EGFR/pWBFNP template with primerpairs C13659/C29538 and C29539/C14288 (BioSource International), inwhich the C29538 and C29539 were phosphorylated with T4 Polynucleotidekinase (NEB, New England Biolabs, Beverly, Mass.):

C13659: (SEQ ID NO: 64)5′-CGGATGAATTCCCAGACCGGACGACAGGCCACCTC-3′(Sense); C29538:(SEQ ID NO: 65) 5′-CTTTCTTTTCCTCCAGAGCC-3′(Anti-Sense); C29539:(SEQ ID NO: 66) 5′-GTAATTATGTGGTGACAGATC-3′(Sense); C14288:(SEQ ID NO: 67) 5′-CGGATCTCGAGCTCAAGAGAGCTTGGTTGGGAGCT-3′ (Anti-Sense).were ligated to introduce a deletion in the sequence encoding aminoacids 6 through 273 of the EGFR extracellular domain and subcloned intoexpression vector pWBDHFR2 (see International Patent Application No. WO99/45031, the disclosure of which is hereby incorporated by reference).

A 232 bp fragment representing the 5′ end of the deletion was generatedwith primer pair C13659/C29538 from Wt-EGFR/pWBFNP template amplifiedwith Pfu polymerase (NEB, New England Biolabs, Beverly, Mass.). The PCRproduct was digested with EcoRl (NEB, New England Biolabs, Beverly,Mass.) and gel purified. A 1273 bp fragment representing the 3′ end ofthe deletion was generated with primer pair C29539/C14288 fromWt-EGFR/pWBFNP and the template amplified with Pfu polymerase. The PCRproduct was digested with XhoI (NEB, New England Biolabs, Beverly,Mass.) and gel purified. Fragments were ligated into EcoRl/Xhol digestedpWBDHFR2 with T4 DNA ligase (NEB, New England Biolabs, Beverly, Mass.)to yield construct EGFRvIII/pWBDHFR

The intracellular domain of EGFR was introduced into the resultingconstruct as follows: A 1566 bp DraIII/XhoI fragment was isolated fromplasmid Wt-EGFR/pWBFNP and ligated into DraIII/XhoI digestedEGFRvIII/pWBDHFR to yield EGFRvIII-FL/pWBDHFR.

3. Transfection of B300.19 Cells with EGFRvIII-FL/pWBDHFR:

B300.19 cells (8×10⁶) were used per transfection in 700 μl DMEM/HImedium. 20 μg EGFRvIII-FL/pWBDHFR and 2 μg CMV-Puro plasmid DNA wereadded. Cells were electroporated at 300 volts/960 uF with Bio-Rad GenePulser. Following electroporation, cells were cooled on ice for 10minutes and, thereafter, 10 ml non-selection medium (DMEM/HI Glucose,10% FBS, 50 μM BME, 2 mM L-Glutamine, 100 units Penicillin-G/ml, 100units MCG Streptomyciniml) was added. Cells were incubated for 48 hrs at37° C. 7.5% CO₂.

Following incubation, cells were split into selection medium (DMEM/HIGlucose, 10% FBS, 2 mM L-Glutamine, 50 μM BME, 100 unitsPenicillin-G/ml, 100 units MCG Streptomycin/ml, 2 ug/ml puromycin) at2×10⁴, 0.4×10⁴′ and 0.08×10⁴ cells/well in 96 well plate and wereselected in selection medium for 14 days to generate stable clones. Puroresistant clones were stained with E752 mAb (an anti-EGFR antibody,described in Yang et al., Crit Rev Oncol Hematol., 38(1):17-23 (2001))and goat anti-human IgG PE then analyzed on FACS Vantage (BectonDickinson).

C. Construction of EGFRvIII-RbFc Expression Constructs.

In order to generate the EGFRvIII rabbit Fe fusion, protein, we firstconstructed a vector containing DNA encoding rabbit Fc. This was ligatedwith DNA encoding EGFRvIII. This approach is described in more detailbelow:

1. Construction of RbFc/pcDNA3.1 Hygro:

Primers 1322/867 (below) were used to amplify a 721 bp fragment encodingthe Hinge-CH2-CH3 domain of rabbit IgG.

#1322 (sense): (SEQ ID NO: 68) 5′-GGTGGCGGTACCTGGACAAGACCGTTGCG-3′#867 (antisense): (SEQ ID NO: 69)5′-ATAAGAATGCGGCCGCTCATTTACCCGGAGAGCGGGA-3′

The resulting PCR product was digested with KpnI and NotI, gel purifiedand ligated into KpnI/NotI digested pcDNA3.1(+)/Hygro (Invitrogen,Burlington, ON) to yield plasmid RbFc/pcDNA3.1 Hygro.

2. Construction of EGFRvIII-RbFc/pCEP4:

Primers 1290/1293 (below) were used to amplify an 1165 bp product fromEGFRvIII-FL/pWBDHFR plasmid template with Pfu polymerase

#1290 (sense): (SEQ ID NO: 70) 5′-CTACTAGCTAGCCACCATGCGACCCTCCGGGA-3′#1293 (anti-sense): (SEQ ID NO: 71) 5′-CGGGGTACCCGGCGATGGACGGGATC-3′

The PCR product was digested with NheI and KpnI, gel purified andligated into NheI/KpnI digested RbFc/pcDNA3.1 Hygro to yield plasmidEGFRvIII-RbFc/pcDNA3.1Hygro.

A 2170 bp SnaBI/XhoI fragment was isolated fromEGFRvIII-RbFc/pcDNA3.1Hygro and subcloned into SnaBI/XhoI digested pCEP4(Invitrogen, Burlington, ON) to yield plasmid EGFRvJII-RbFc/pCEP4.

3. Generation of 293F EGFRvIII-RbFc Stable Cell Lines:

Plasmid EGFRvIII-RbFc/pCEP4 was introduced into 293F cells (Gibco, GrandIsland, N.Y.) by Calcium Phosphate transfection, as follows: one dayprior to transfection, 1×10⁶293 F cells were plated on a gelatin coated100 mm tissue culture petridish and incubated at 5% CO2, 37° C. Cellswere fed with 10 ml of fresh non-selective media (DMEM/F12, 10% FBS, 2mM L-Glutamine, 100 U/ml Penicillin G, 100 U/ml MCG Streptomycin) 2-3hours before transfection. Transfection reagents were prepared in amicrofuge tube, as follow: 10 μg of DNA (EGFRvIII-RbFc/pCEP4) was mixedwith 62 μl of 2M Calcium Phosphate and deionized water to make the finalvolume 5041. In another tube pipette 500 μl of 2×HBS is drawn and usedto transfer the transfection reagents.

The solution in the tube pipette was added to the cells drop by drop,while maintaining proper pH by leaving cells in a 5% CO2 incubator untiltransfection was performed. 15-20 hours after transfection, cells werewashed with PBS and feed with 10 ml of fresh 293F non-selective media.Expressing cells were harvested with trypsin 48-72 post-transfection andcells were plated at 0.08×10⁴ cells/well in a 96 well plate in 293Fselective media (DMEM/F12, 10% FBS, 2 mM L-Glutamine, 100 U/mlPenicillin G, 100 U/ml MCG Streptomycin, 250 ug/ml Hygromycin) for 14days.

Hygromycin resistent clones were screened by ELISA using anti-EGFRantibody E763 (U.S. Pat. No. 6,235,883) as the capture antibody at 1ug/ml and detecting with a goat anti-rabbit IgG HRPO (CalTag) at 1:100dilution.

Example 2 Production of Anti-EGFRvIII Antibodies Through HybridomaGeneration

Eight XenoMouse mice that produce antibodies with a gamma-1 constantregion (XenoMouse G1 mice) were immunized on day 0 and boosted on days11, 21, 32, 44 and 54 for this protocol and fusions were performed onday 58. All immunizations were conducted via subcutaneous administrationat the base of tail plus intraperitoneal administartion for allinjections. The day 0 immunization was done with 1.5×10⁷B300.19/EGFRvIII transfected cells (Example 1A) suspended in pyrogenfree DPBS admixed 1:1 v/v with complete Freunds adjuvant (CFA) (Sigma,St. Louis, Mo.). Boosts on days 11, 21, and 32 were done with 1.5×10⁷B300.19/EGFRvIII transfected cells in DPBS admixed 1:1 v/v withincomplete Freunds adjuvant (IFA) (Sigma, St. Louis, Mo.). The boosts onday 44 was done with 5 μg of the PEP3 (EGFRvIII peptide)—KLH conjugate(Example 1) in DPBS admixed 1:1 v/v with IFA and final boost, on day 54,was done with 5 ug PEP3 (EGFRvIII peptide)—KLH conjugate in DPBS withoutadjuvant.

On day 58, mice were euthanized, and then inguinal and Lumbar lymphnodes were recovered. Lymphocytes were released by mechanical disruptionof the lymph nodes using a tissue grinder then depleted of T cells byCD90 negative selection. The fusion was performed by mixing washedenriched B cells and non-secretory myeloma P3X63Ag8.653 cells purchasedfrom ATCC, cat. # CRL 1580 (Kearney et al, J. Immunol. 123:1548-1550(1979)) at a ratio of 1:1. The cell mixture was gently pelleted bycentrifugation at 800 g. After complete removal of the supernatant, thecells were treated with 2-4 mL of Pronase solution (CalBiochem, cat.#53702; 0.5 mg/ml in PBS) for no more than 2 minutes. Then, 3-5 ml ofFBS was added to stop the enzyme activity and the suspension wasadjusted to 40 ml total volume using electro cell fusion solution, ECFS(0.3M Sucrose, Sigma, Cat # S7903, 0.1 mM Magnesium Acetate, Sigma, Cat# M2545, 0.1 mM Calcium Acetate, Sigma, Cat # C4705 (St. Louis, Mo.)).

The supernatant was removed after centrifugation and the cells washed byresuspension in 40 ml ECFS. This wash step was repeated and the cellsagain were resuspended in ECFS to a concentration of 2×10⁶ cells/ml.Electro-cell fusion was performed using a fusion generator, modelECM2001, Genetronic, Inc., San Diego, Calif. The fusion chamber sizeused was 2.0 ml, and using the following instrument settings: Alignmentcondition: voltage: 50 v, time: 50 s, Membrane breaking at: voltage:3000 v, time: 30 μs, Post-fusion holding time: 3 s. After fusion, thecells were re-suspended in DMEM (JRH Biosciences), 15% FCS (Hyclone),containing HAT, and supplemented with L-glutamine, pen/strep, OPI(oxaloacetate, pyruvate, bovine insulin) (all from Sigma, St. Louis,Mo.) and IL-6 (Boehringer Mannheim) for culture at 37° C. and 10% CO² inair.

Cells were plated in flat bottomed 96-well tissue culture plates at4×10⁴ cells per well. Cultures were maintained in HAT (hypoxanthine,aminopterin and thymidine) supplemented media for 2 weeks beforetransfer to HT (hypoxanthine and thymidine) supplemented media.Hybridomas were selected for by survival in HAT medium and supernatantswere screened for antigen reactivity by ELISA. The ELISA format entailedincubating supernatants on antigen coated plates (EGFRvIII peptide-OVAcoated plates and wild type EGFr peptide-OVA coated plates as a counterscreen) and detecting EGFRvIII-specific binding using horseradishperoxidase (HRP) labeled mouse anti-human IgG (see Table 2.1).

TABLE 2.1 1^(st) OD 2^(nd) OD Plate.Well Hybridoma fusion plate muEGFrEGFr 13.2 D10 13.1 4.034 2.653 0.051 13.3 C12 13.2 3.829 2.443 0.04913.3 F11 13.3 3.874 1.081 0.049 13.6 B11 13.4 3.322 1.311 0.052 OD #1 OD#2 Clones Plate cloning plate muEGFr EGFr 13.1.1 0.5c/w D2 2.614 2.5860.042 13.1.2 0.5c/w F5 2.248 1.272 0.041

As will be observed, at least four antigen specific hybridomas weredetected: 13.1, 13.2, 13.3, and 13.4. These hybridomas that werepositive in the ELISA assay EGFRvIII specificity were confirmed by FACSon stably transfected 300.19 cells expressing EGFRvIII versus 300.19untransfected parental cells.

Cloning was performed on selected antigen-positive wells using limiteddilution plating. Plates were visually inspected for the presence ofsingle colony growth and supernatants from single colony wells thenscreened by antigen-specific ELISAs and FACS confirmation as describedabove. Highly reactive clones were assayed to verify purity of humangamma and kappa chain by multiplex ELISA using a Luminex instrument.Based on EGFRvIII specificity in the ELISA and FACS assay, Clone 13.1.2was selected as the most promising candidate for further screening andanalysis. The nucleotide and amino acid sequences of the heavy and lightchains of 13.1.2 antibody are shown in FIG. 3L and SEQ ID NO: 137 and139 for heavy and light chain nucleic acids and 138 and 140 for heavyand light chain amino acid sequences. In addition, a comparison of the13.1.2 heavy chain and light chain sequences with the germline sequencefrom which they were derived as shown in FIGS. 4 and 5.

Example 3 Antibody Generation Through Use of Xenomax Technology

Immunization of XenoMouse Animals

Human monoclonal antibodies against human EGFRvIII were developed bysequentially immunizing XenoMouse mice that produce antibodies with agamma-1 constant region (XenoMouse G1 mice), XenoMouse mice that produceantibodies with gamma-2 constant regions (XenoMouse XMG2 mice), andXenoMouse mice that produce antibodies with a gamma-4 constant region(XenoMouse G4 mice).

To generate mAbs by through XenoMax technology, cohorts of XenoMouse G1and XMG2 mice were immunized with EGFRvIII PEP3 (Example 1A) andEGFRvIII-expressing 300.19 cells (Example 1B) or with bacteriallyexpressed extracellular domain of EGFRvIII protein (EGFRvIII-ECD) (Dr.Bigner, Duke University) and EGFRvIII-expressing 300.19 cells or withEGFRvIII-Rabbit Fc fusion protein (EGFRvIII-RbFc) (Example 1C) andEGFRvIII-expressing 300.19 cells or with EGFRvIII-RbFc only via foot pad(FP), or via base of the tail by subcutaneous injection andintraperitoneum (BIP).

For footpad immunizations, the initial immunization was with or without10×10⁶ EGFRvIII-expressing 300.19 cells and with or without 10 μg ofEGFRvIII PEP3 or EGFRvIII-ECD or EGFRvIII-RbFc mixed 1:1 v/v withTitermax gold (Sigma, Oakville, ON) per mouse. The subsequent boostswere performed with half of the amount of immunogen used in the initialimmunization. The first four boosts were done by taking the immunogenmixed with alum (Sigma, Oakville, ON), adsorbed overnight, per mouse asshown in the Table 3.1 below. This was followed by one injection withthe respective immunogen in Titermax gold, one injection with alum andthen a final boost of the immunogen in PBS as shown in Table 3.1. Inparticular, animals were immunized on days 0, 3, 7, 10, 14, 17, 21 and24. The animals were bled on day 19 to obtain sera and determine thetiter for harvest selection. The animals were harvested on Day 28.

TABLE 3.1 Footpad immunization schedule Group # 1 2 3 4 5 6 7 8 # ofanimals 5 5 5 5 5 5 5 5 Mouse strain XMG2 XM3C-3 XMG2 XM3C-3 XMG2 XM3C-3XMG2 XM3C-3 Boost # Adjuvant Immunogen Immunogen Immunogen Immunogen1^(st) Titermax EGFRvIII- EGFRvIII- EGFRvIII- EGFRvIII-RbFc gold 300.19cells + 300.19 cells + 300.19 cells + PEP3-KLH EGFRvIII-ECDEGFRvIII-RbFc 2^(nd) Alum EGFRvIII- EGFRvIII- EGFRvIII- EGFRvIII-RbFc300.19 cells 300.19 cells 300.19 cells 3^(rd) Alum PEP3-KLH EGFRvIII-ECDEGFRvIII-ECD EGFRvIII-RbFc 4^(th) Alum EGFRvIII- EGFRvIII- EGFRvIII-EGFRvIII-RbFc 300.19 cells 300.19 cells 300.19 cells 5^(th) AlumPEP3-KLH EGFRvIII-ECD EGFRvIII-ECD EGFRvIII-RbFc 6^(th) TitermaxEGFRvIII- EGFRvIII- EGFRvIII- EGFRvIII-RbFc gold 300.19 cells 300.19cells 300.19 cells 7^(th) Alum PEP3-KLH EGFRvIII-ECD EGFRvIII-ECDEGFRvIII-RbFc 8^(th) PBS EGFRvIII- EGFRvIII- EGFRvIII- EGFRvIII-RbFc300.19 cells + 300.19 cells + 300.19 cells + PEP3-KLH EGFRvIII-ECDEGFRvIII-RbFc Harvest

The initial BIP immunization with the respective immunogen, as describedfor the footpad immunization, was mixed 1:1 v/v with Complete Freund'sAdjuvant (CFA, Sigma, Oakville, ON) per mouse. Subsequent boosts weremade first with the immunogen respectively, mixed 1:1 v/v withIncomplete Freund's Adjuvant (IFA, Sigma, Oakville, ON) per mouse,followed by a final boost in PBS per mouse. The animals were immunizedon days 0, 14, 28, 42, 56, and day 75 (final boost) as shown in Table3.2 below. The animals were bled on day 63 to obtain sera and determinethe titer for harvest selection. The animals were harvested on Day 78.

TABLE 3.2 Bip Immunization schedule Group 9 10 11 12 13 14 15 16 # ofanimals 5 5 5 5 5 5 5 5 Mouse strain XMG2 XM3C-3 XMG2 XM3C-3 XMG2 XM3C-3XMG2 XM3C-3 Boost # Adjuvant Immunogen Immunogen Immunogen Immunogen1^(st) CFA EGFRvIII- EGFRvIII- EGFRvIII- EGFRvIII-RbFc 300.19 cells +300.19 cells + 300.19 cells + PEP3-KLH EGFRvIII-ECD EGFRvIII-RbFc 2^(nd)IFA EGFRvIII- EGFRvIII- EGFRvIII- EGFRvIII-RbFc 300.19 cells 300.19cells 300.19 cells 3^(rd) IFA PEP3-KLH EGFRvIII-ECD EGFRvIII-ECDEGFRvIII-RbFc 4^(th) IFA EGFRvIII- EGFRvIII- EGFRvIII- EGFRvIII-RbFc300.19 cells 300.19 cells 300.19 cells 5^(th) IFA PEP3-KLH EGFRvIII-ECDEGFRvIII-ECD EGFRvIII-RbFc 6^(th) PBS EGFRvIII- EGFRvIII- EGFRvIII-EGFRvIII-RbFc 300.19 cells + 300.19 cells + 300.19 cells + PEP3-KLHEGFRvIII-ECD EGFRvIII-RbFc Harvest

Selection of Animals for Harvest by Titer Determination

Anti-hEGFRvIII antibody titers were determined by ELISA. EGFRvIII-RbFc(2.5 μg/ml) or a control RbFc (2 μg/ml) or EGFRvIIIpeptide-OVA (2 μg/ml)(Example 1) or control OVA (4 μg/ml) were coated onto Costar LabcoatUniversal Binding Polystyrene 96-well plates (Corning, Acton, Mass.)overnight at four degrees. The solution containing unbound antigen wasremoved and the plates were treated with UV light (365 nm) for 4 minutes(4000 microjoules). The plates were washed five times with dH₂O. Serafrom the EGFRvIII immunized XenoMouse® animals, or naïve XenoMouse®animals, were titrated in 2% milk/PBS at 1:2 dilutions in duplicate froma 1:100 initial dilution. The last well was left blank. The plates werewashed five times with dH₂O. A goat anti-human IgG Fc-specifichorseradish peroxidase (HRP, Pierce, Rockford, Ill.) conjugated antibodywas added at a final concentration of 1 μg/mL for 1 hour at roomtemperature. The plates were washed five times with dH₂O. The plateswere developed with the addition of TMB chromogenic substrate(Gaithersburg, Md.) for 30 minutes and the ELISA was stopped by theaddition of 1 M phosphoric acid. The specific titer of individualXenoMouse® animals was determined from the optical density at 450 nm andis shown in Tables 3.3 and 3.4. The titer represents the reciprocaldilution of the serum and therefore the higher the number the greaterthe humoral immune response to hEGFRvIII.

For the mice immunized via base of the tail by subcutaneous injectionand intraperitoneum, the titre was determined exactly as above exceptthe plates were coated with EGFRvIII-RbFc (2.0 μg/ml) or a control RbFc(2.5 μg/ml).

TABLE 3.3 EGFRvIII Immunization Mouse EGFRvIII- Control peptide- OVAGroup (site and Strain Mouse RbFc @ RbFc @ OVA coated coated at #Immunogen) and sex I.Ds 2.5 ug/ml. 2.0 ug/ml. at 2.0 μg/ml 4.0 μg/ml 1FP XMG2 0748-1 330 13549 <100 EGFRvIII- 0748-2 237 7635 <100 300.19cells + 0748-3 109 9824 <100 EGFRvIII 0748-4 714 8014 <100 PEP3-KLH (see0748-5 165 9421 <100 Imm. Sched.) Naïve <100 n/a n/a 2 FP XM3C-3 0741-1388 347 <100 EGFRvIII- 0741-2 327 240 <100 300.19 cells + 0741-3 385 330<100 EGFRvIII 0741-4 589 227 <100 PEP3-KLH (see 0741-5 273 626 <100 Imm.Sched.) Naïve <100 n/a n/a 3 FP XMG2 0749-1 552 <100 <100 EGFRvIII-0749-2 477 <100 <100 300.19 cells + 0749-3 100 <100 <100 EGFRvIII-0749-4 100 <100 <100 ECD (see 0749-5 1631 <100 <100 Imm. Sched.) Naïve100 n/a n/a 4 FP XM3C-3 0742-1 372 <100 <100 EGFRvIII- 0742-2 745 <100<100 300.19 cells + 0742-3 484 <100 <100 EGFRvIII- 0742-4 530 <100 <100ECD (see 0742-5 270 <100 <100 Imm. Sched.) Naïve 100 n/a n/a 5 FP XMG20750-1 5399 175 <100 <100 EGFRvIII- 0750-2 3072 151 <100 <100 300.19cells + 0750-3 >6400 358 <100 <100 EGFRvIII- 0750-4 5845 196 <100 <100RbFc (see 0750-5 5770 196 <100 <100 Imm. Sched.) Naïve 100 100 n/a n/a 6FP XM3C-3 0743-1 1220 <100 <100 <100 EGFRvIII- 0743-2 1183 <100 <100<100 300.19 cells + 0743-3 645 <100 <100 <100 EGFRvIII- 0743-4 759 <100<100 <100 RbFc (see 0743-5 1260 <100 <100 <100 Imm. Sched.) Naïve 100<100 n/a n/a 7 FP XMG2 0745-1 1897 <100 <100 <100 EGFRvIII- 0745-2 >6400323 <100 <100 RbFc (see 0745-3 1225 <100 <100 <100 Imm. Sched.) 0745-44047 <100 <100 <100 0745-5 852 <100 <100 <100 Naïve 100 <100 n/a n/a 8FP XM3C-3 0744-1 362 <100 <100 <100 EGFRvIII- 0744-2 807 <100 <100 <100RbFc (see 0744-3 479 <100 <100 <100 Imm. Sched.) 0744-4 631 <100 <100<100 0744-5 1112 <100 <100 <100 Naïve 100 <100 n/a n/a

All the XenoMouse animals from group 5 and XenoMouse animals 0743-5 fromgroup 6 from Table 3.3 were selected for XenoMax harvests based on theserology.

TABLE 3.4 EGFRvIII Immunization Mouse EGFRvIII- Control peptide- OVAGroup (site and Strain Mouse RbFc @ RbFc @ OVA coated coated at #Immunogen) and sex I.Ds 2.0 ug/ml. 2.5 ug/ml. at 2.0 μg/ml 4.0 μg/ml 9BIP XMG2 O695-1 2921 >128000 472 EGFRvIII- O695-2 2219 30504 379 300.19cells + O695-3 4609 >128000 608 EGFRvIII O695-4 >6400 >128000 368PEP3-KLH (see O695-5 1580 19757 269 Imm. Sched.) Naïve <100 n/a 242 10BIP XM3C-3 O700-1 <100 EGFRvIII- O700-2 <100 300.19 cells + O700-3 >6400EGFRvIII O700-4 5342 PEP3-KLH (see O700-5 >6400 Imm. Sched.) Naïve <10011 BIP XMG2 O696-1 <100 561 240 EGFRvIII- O696-2 <100 788 326 300.19cells + O696-3 <100 604 266 EGFRvIII- O696-4 143 444 263 ECD (see O696-5<100 303 254 Imm. Sched.) Naïve <100 242 12 BIP XM3C-3 O702-1 358EGFRvIII- O702-2 469 300.19 cells + O702-3 401 EGFRvIII- O702-4 >6400ECD (see O702-5 >6400 Imm. Sched.) Naïve <100 13 BIP XMG2O694-1 >6400 >6400 250 243 EGFRvIII- O694-2 >6400 >6400 296 309 300.19cells + O694-3 >6400 >6400 736 605 EGFRvIII- O694-4 >6400 >6400 739 1111RbFc (see O694-5 3710 >6400 517 465 Imm. Sched.) Naïve <100 >6400 242 14BIP XM3C-3 O703-1 2740 >6400 EGFRvIII- O703-2 408 >6400 300.19 cells +O703-3 1406 >6400 EGFRvIII- O703-4 1017 >6400 RbFc (see O703-5 403 >6400Imm. Sched.) Naïve <100 >6400 15 BIP XMG2 O697-1 >6400 >6400 340 348EGFRvIII- O697-2 >6400 >6400 642 1793 RbFc (see O697-3 6242 >6400 319246 Imm. Sched.) O697-4 1766 >6400 133 <100 O697-5 >6400 >6400 685 448Naïve <100 >6400 243 242 16 BIP XM3C-3 O701-1 592 >6400 EGFRvIII- O701-21118 >6400 RbFc (see O701-3 >6400 >6400 Imm. Sched.) O701-4 <100 <100O701-5 n/a n/a Naïve <100 >6400

XenoMouse animals (0695-1, 0695-3 and 0695-4) were selected for harvestsbased on the serology data in Table 3.4.

Selection of B cells.

B-cells from the above-discussed animals were harvested and cultured.Those secreting EGFRvIII-peptide specific antibodies were isolated asdescribed in Babcook et al., Proc. Natl. Acad. Sci. USA, 93:7843-7848(1996). ELISA was used to identify primary EGFRvIII-peptide-OVA-specificwells. About 5 million B-cells were cultured from XenoMouse animals in245 96 well plates at 500 or 150 or 50 cells/well, and were screened onEGFRvIII-peptide-OVA to identify the antigen-specific wells. About 515wells showed ODs significantly over background, a representative sampleof which are shown in Table 3.5.

TABLE 3.5 Total # of Positives above cutoff OD of: plates 0.0 0.1 0.20.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.5 2.0 2.5 3.0 3.5 Cansera 12 1152 63481 56 49 45 38 32 29 26 25 18 11 4 1 0 500 cells/well Sigma 13 1248 773195 139 117 99 80 73 58 53 49 21 9 5 1 0 500 cells/well Sigma 20 19201304 478 178 91 67 55 47 45 36 33 19 9 5 2 0 150 cells/well Total 454320 2711 754 373 257 211 173 152 132 115 107 58 29 14 4 0

244 of EGFRvIII-peptide-OVA-Elisa positive wells of OD >0.5 werescreened again on EGFRvIII-peptide-OVA and on OVA to confirm that theywere EGFRvIII-peptide specific. A representative example of theseresults is shown in Table 3.6.

TABLE 3.6 1′ EGFRvIII 2′ EGFRvIII peptide-OVA peptide-OVA OVA Plate WellOD OD OD 121 G 1 0.7534 1.4065 0.1355 121 A 7 1.3472 2.1491 0.1268 121 D8 0.6743 0.4179 0.1531 121 E 8 2.0415 2.6965 0.1498 121 H 10 0.86110.4288 0.1595 121 C 12 2.1455 2.6443 0.1404 122 H 1 1.8890 2.5987 0.1164122 H 5 0.5943 0.8321 0.1572 122 F 8 0.6834 0.7715 0.1450

Limited Antigen Assay and Analysis

The limited antigen analysis is a method that affinity-ranks theantigen-specific antibodies present in B-cell culture supernatantsrelative to all other antigen-specific antibodies. In the presence of avery low coating of antigen, only the highest affinity antibodies shouldbe able to bind to any detectable level at equilibrium. (See, e.g.,International Patent Application No. WO 03/48730)

EGFRvIII peptide-OVA was coated to plates at three concentrations; 7.5ng/ml, 1.5 ng/ml and 0.03 ng/ml for overnight at 4° C. on 96-well Elisaplates. Each plate was washed 5 times with dH₂O, before 50 ul of 1% milkin PBS with 0.05% sodium azide were added to the plate, followed by 4 μlof B cell supernatant added to each well. After 18 hours at roomtemperature on a shaker, the plates were again washed 5 times with dH₂O.To each well was added 50 ul of Gt anti-Human (Fc)-HRP at 1 μg/ml. After1 hour at room temperature, the plates were again washed 5 times withdH₂O and 50 μl of TMB substrate were added to each well. The reactionwas stopped by the addition of 50 uL of 1M phosphoric acid to each welland the plates were read at wavelength 450 nm and the results shown inTable 3.7.

TABLE 3.7 High Cul- Limited Ag Antigen ture 0.03 ng/ml 1.5 ng/ml 7.5ng/ml (1.0 Plate Well OD Rank OD Rank OD Rank μg/ml) 133 B 2 0.7670 11.189 54 1.871 95 2.050 124 G 12 0.7400 2 1.895 1 3.101 1 3.463 145 C 10.715 3 1.552 7 2.671 10 3.194 129 G 10 0.6720 4 1.367 22 2.692 8 2.977186 B 6 0.657 5 1.842 2 2.859 3 3.411 143 F 12 0.653 6 1.677 3 2.741 63.156 136 E 3 0.6340 7 1.468 15 2.683 9 3.280 137 C 11 0.595 8 1.582 52.94 2 3.444 139 A 11 0.582 9 1.374 19 2.282 47 2.255 174 F 1 0.573 101.577 6 2.775 4 2.364

The results generated from limited antigen analysis were compared to thetotal OD obtained in high antigen assay. A relative ranking of affinitywas done by taking the ratio of the OD obtained in limited antigen assayVs that obtained in high antigen assay. Antibodies with higher ratiowill have the highest affinity. Table 3.7 shows the sample of B-cellculture supernatants that were ranked based on limited antigen assay OD(for the lowest antigen plating concentration of 0.03 ng/ml) Vs the highantigen assay OD.

Native Cell Binding Assay by FMAT

EGFRvIII peptide-OVA-Elisa positive well supernatants were analyzed fortheir ability to bind to the native form of EGFRvIII stably expressed onNR6 cells (NR6 M cells) (See, Batra et al. Epidermal growth factorligand-independent, unregulated, cell-transthnning potential of anaturally occurring human mutant EGFRvIII gene. Cell Growth Differ.6(10):1251-9 (1995)). NR 6 lvi cells were seeded at 8000 cells per welland incubated over night in 96 well FMAT plates. Media was then removedleaving 15 μl in the well. 15 μl B-cell culture supernatants were addedand 15 μl anti-human IgG Fc Cy5 at 1 μg/ml final concentration added towells. It is then left incubated at 4° C. for 2 hours. The cells werewashed with 150 μl PBS, and fixed before reading on FMAT. The resultswere expressed as total fluorescent intensity (Table 3.8). Humananti-EGFRvIII mAb 13.1.2 was used as a positive control starting at 1μg/ml final concentration and negative control was PK 16.3.1 at the sameconcentration. 134 of the 244 samples tested bound to NR6M cells ofwhich 62 had a total fluorescence of greater than 8000. 6 of these 134binders were false positives.

The same type of native binding assay was done on NR6 Wt cells (NR6cells expressing EGF receptor) (See Batra et al. Epidermal growth factorligand-independent, unregulated, cell-transforming potential of anaturally occurring human mutant EGFRvIII gene. Cell Growth Differ.6(10):1251-9 (1995)) to eliminate the binding is due to binding to Wtreceptor (Table 3.8). ABX-EGF was used as a positive control and PK16.3.1 at the same concentration was used as a negative controlantibody. 3 out the 134 NR6 M binders were binding strongly to NR6 Wtcells. 190 of the 244 wells bound EGFRvIII peptide in Elisa were alsohound to the native form on cells. Examples are given in Table 3.8.

TABLE 3.8 FMAT FMAT native native 1′ VIII- 2′ VIII- binding bindingpep-OVA pep-OVA OVA to NR6 to NR6 Plate OD OD OD M cells Wt cells 174 F1 2.4945 3.0308 0.1900 138373 1668 187 A 4 1.5337 1.2085 0.1920 128626202459.8 132 D 8 0.8555 1.2070 0.1649 109379 0 142 C 11 2.2889 2.81940.2239 94944 0 129 A 7 2.1501 2.8208 0.1515 84024 0 127 E 1 2.69233.1986 0.1219 82031 0 124 G 12 3.2929 3.5634 0.1455 73080 0 141 C 60.7512 1.2567 0.1547 60816 814.5 173 C 1 2.5728 2.5714 0.2134 587022523.4 128 G 9 0.6293 0.7483 0.1520 49631 0 129 H 6 2.9370 3.0952 0.25820 0 183 E 11 2.3450 2.7717 0.1050 0 0

In Table 3.8, supernatant from well 187A4 is identified as a Wt binderand 14106 was a false positive for NR6 M cells binding. Wells 129H6 and183E11 are strong peptide binders with no native binding.

Internalization Assay

The top 60 native binding B cell culture supernatants were furtherassayed for their ability to internalize the receptor. NR6 M cells wereseeded at 8000 cells/well into 96 well FMAT plates and incubatedovernight. Media was removed and 10-15 μl B-Cell culture supernatant ina total volume of 30 μl media, in duplicate was added. Next, 15 μl ofsecondary antibody (SS Alexa 647 anti-human IgG Fab at 1.5 μg/ml finalconcentration) was added and the mixture was incubated on ice for 1 hr.An irrelevant B-Cell Culture supernatant was used to see the effect ofthe culture media. Human anti-EGFRvIII mAb 13.2.1 was used as a positivecontrol starting at 1 μg/ml (final concentration) and negative controlwas PK 16.3.1 (human anti-KLH IgG2 antibody) at the same concentration.After incubation, the cells were washed with cold PBS, 50 μl media wasadded to all of the wells, one of the duplicates were incubated at 37°C. for 30 mins while the other duplicate remained on ice. After theincubations media was removed, 100 ul of cold 50 mM glutathione wasadded to the set incubated at 37° C. and 100 μl of cold media added tothe other set, both sets were then left on ice for 1 hr. The cells werethen washed with 100 μl cold PBS and then fixed with 1% paraformaldehydeand read in FMAT. The results were expressed as % internalized,calculated as total fluorescence in the presence of glutathione/totalfluorescence in the absence of glutathione×100. Representativeinformation is given in Table 3.9.

TABLE 3.9 % No With internalized, glutathione glutathione (glut+/ Wellno. FL1xcount FL1xcount glut−) × 100 124 C9 1877 1394 74.3% 124 G1226465 9959 37.6% 125 H1 14608 3686 25.2% 125 D10 2342 1236 52.8% 127 E115059 1318 8.7% 127 B9 12444 7109 57.1% 127 E11 6623 0 0.0% 128 G9 100711851 18.4% 129 A7 27648 8708 31.5% 130 B4 4558 4354 95.5% 131 H5 92582656 28.7% 132 D8 35820 13293 37.1% 133 F9 9773 3621 37.0% 136 F10 23920 0.0% 137 G6 5104 1021 20.0% 137 G10 3451 0 0.0%

EGFRvIII-specific Hemolytic Plaque Assay.

A number of specialized reagents were needed to conduct this assay.These reagents were prepared as follows.

1. Biotinylation of Sheep red blood cells (SRBC).

SRBCs were stored in RPMI media as a 25% stock. A 250 μl SRBCpacked-cell pellet was obtained by aliquoting 1.0 ml of SRBC to a fresheppendorf tube. The SRBC were pelleted with a pulse spin at 8000 rpm(6800 ref) in microfuge, the supernatant drawn off, the pelletre-suspended in 1.0 ml PBS at pH 8.6, and the centrifugation repeated.The wash cycle was repeated 2 times, then the SRBC pellet wastransferred to a 15-ml falcon tube and made to 5 ml with PBS pH 8.6. Ina separate 50 ml falcon tube, 2.5 mg of Sulfo-NHS biotin was added to 45ml of PBS pH 8.6. Once the biotin had completely dissolved, the 5 ml ofSRBCs were added and the tube rotated at RT for 1 hour. The SRBCs werecentrifuged at 3000 rpm for 5 min and the supernatant drawn off. Thebiotinylated SRBCs were transferred to an eppendorf tube and washed 3times as above but with PBS pH 7.4 and then made up to 5 ml with immunecell media (RPMI 1640) in a 15 ml falcon tube (5% B-SRBC stock). Stockwas stored at 4° C. until needed.

2. Streptavidin (SA) coating of B-SRBC.

1 ml of the 5% B-SRBC stock was transferred into a fresh eppendorf tube.The B-SRBC cells were washed 3 times as above and resuspended in 1.0 mlof PBS at pH 7.4 to give a final concentration of 5% (v/v). 10 μl of a10 mg/ml streptavidin (CalBiochem, San Diego, Calif.) stock solution wasadded and the tube mixed and rotated at RT for 20 min. The washing stepswere repeated and the SA-SRBC were re-suspended in lml PBS pH 7.4 (5%(v/v)).

3. EGFRvIII coating of SA-SRBC.

The SA-SRBCs were coated with biotinylated-EGFRvIIIpetide-OVA at 10μg/ml, mixed and rotated at RT for 20 min. The SRBC were washed twicewith 1.0 ml of PBS at pH 7.4 as above. The EGFRvIII-coated SRBC werere-suspended in RPMI (+10% FCS) to a final concentration of 5% (v/v).

4. Determination of the quality of EGFRvHIIIpeptide-SRBC byimmunofluorescence (IF).

10 μl of 5% SA-SRBC and 10 μl of 5% EGFRvIII peptide-coated SRBC wereeach added to a separate fresh 1.5 ml eppendorf tube containing 40 ul ofPBS. A control human anti-EGFRvIII antibody was added to each sample ofSRBCs at 45 μg/ml. The tubes were rotated at RT for 25 min, and thecells were then washed three times with 100 μl of PBS. The cells werere-suspended in 50 μl of PBS and incubated with 40 mcg/mL Gt-anti HumanIgG Fc antibody conjugated to Alexa488 (Molecular Probes, Eugene,Oreg.). The tubes were rotated at RT for 25 min, and then washed with100 μl PBS and the cells re-suspended in 10 μl PBS. 10 μl of the stainedcells were spotted onto a clean glass microscope slide, covered with aglass coverslip, observed under fluorescent light, and scored on anarbitrary scale of 0-4.

5. Preparation of plasma cells.

The contents of a single microculture well previously identified byvarious assays as containing a B cell clone secreting the immunoglobulinof interest were harvested. Using a 100-1000 μl pipetman, the contentsof the well were recovered by adding 37 C RPMI (10% FCS). The cells werere-suspended by pipetting and then transferred to a fresh 1.5 mleppendorf tube (final vol. approx 500-700 μl). The cells werecentrifuged in a microfuge at 2500 rpm (660 rcf) for 1 minute at roomtemperature, and then the tube was rotated 180 degrees and spun againfor 1 minute at 2500 rpm. The freeze media was drawn off and the immunecells resuspended in 100 μl RPMI (10% FCS), then centrifuged. Thiswashing with RPMI (10% FCS) was repeated and the cells re-suspended in60 RPMI (10% FCS) and stored on ice until ready to use.

6. Micromanipulation of plasma cells. Glass slides (2×3 inch) wereprepared in advance with silicone edges and allowed to cure overnight atRT. Before use, the slides were treated with approx. 5 ul of SigmaCoat(Sigma, Oakville, ON) wiped evenly over glass surface, allowed to dryand then wiped vigorously. To a 60 μl sample of cells was added 60 μleach of EGFRvIIIpeptide-coated SRBC (5% v/v stock), 4× guinea pigcomplement (Sigma, Oakville, ON) stock prepared in RPMI (10% FCS), and4× enhancing sera stock (1:150 in. RPMI with 10% FCS). The mixture wasspotted (10-15 μl) onto the prepared slides and the spots covered withundiluted paraffin oil. The slides were incubated at 37° C. for aminimum of 45 minutes. The EGFRvIII-specific plasma cells wereidentified from plaques and rescued by micromanipulation (see Table3.10).

TABLE 3.10 Total number of Well ID Single Cell Number Single cellspicked 124 G 12 EGFRvIII-SCX-105-116(LL) 12 129 A 7 EGFRvIII-SCX-117-128(DM) 12 174 F 1 EGFRvIII-SCX-129-137 (DM) 9 182 A 5 EGFRvIII-SCX-138-149(LL); 20 162-169 (OP) 125 D 10 EGFRvIII-SCX-170-181 (DM); 20 194-201(LL) 127 B 9 EGFRvIII-SCX-182-193 (LL); 20 202-209 (OP) 190 D 7EGFRvIII-SCX-210-229 (LL) 20 130 B 4 EGFRvIII-SCX-230-249 (LL) 20 138 D2 EGFRvIII-SCX-250-269 (LL) 20 145 C 1 EGFRvIII-SCX-80-92 (DM) 13 172 B12 EGFRvIII-SCX-93-104 (LL) 12 187 A 4 EGFRvIII-SCX-270-281 (LL) 12 173C 1 EGFRvIII-SCX-282-293 (BC) 12 127 E 1 EGFRvIII-SCX-294-305 (LL) 12142 C 11 EGFRvIII-SCX-306-317 (LL) 12 141 A 10 EGFRvIII-SCX-318-329 (BC)12 132 D 8 EGFRvIII-SCX-330-341 (LL) 12 124 D 4 EGFRvIII-SCX-342-349(BC) 8

Single cell PCR, Cloning, Expression, Purification and Characterizationof Recombinant anti-EGFRvIII Antibodies.

The genes encoding the variable regions were rescued by RT-PCR on thesingle micromanipulated plasma cells. mRNA was extracted and reversetranscriptase PCR was conducted to generate cDNA. The cDNA encoding thevariable heavy and light chains was specifically amplified usingpolymerase chain reaction. The human variable heavy chain region wascloned into an IgG1 expression vector. This vector was generated bycloning the constant domain of human IgG1 into the multiple cloning siteof pcDNA3.1+/Hygro (Invitrogen, Burlington, ON). The human variablelight chain region was cloned into an IgK expression vector. Thesevectors were generated by cloning the constant domain of human IgK intothe multiple cloning site of pcDNA3.1+/Neo (Invitrogen, Burlington, ON).The heavy chain and the light chain expression vectors were thenco-lipofected into a 60 mm dish of 70% confluent human embryonal kidney293 cells and the transfected cells were allowed to secrete arecombinant antibody with the identical specificity as the originalplasma cell for 24-72 hours. The supernatant (3 mL) was harvested fromthe HEK 293 cells and the secretion of an intact antibody wasdemonstrated with a sandwich ELISA to specifically detect human IgG(Table 3.11). Specificity was assessed through binding of therecombinant antibody to EGFRvIII using ELISA (Table 3.11).

TABLE 3.11 Titer Total Antigen mAb ID Cell # antibody binding 129A7SC-EGFRvIII-XG1-123/124 >1:64 >1:64 138D2SC-EGFRvIII-XG1-250 >1:64 >1:64 174F1 SC-EGFRvIII-XG1-131 >1:64 >1:64182A5 SC-EGFRvIII-XG1-139 >1:64 >1:64 190D7SC-EGFRvIII-XG1-211 >1:64 >1:64 125D10 SC-EGFRvIII-XG2-170 >1:64 >1:64182D5 SC-EGFRvIII-XG2-150 >1:64 >1:64 141A10 SC-EGFRvIII-XG1-318  1:64 1:64 132D8 SC-EGFRvIII-XG1-333 >1:64 >1:64 124D4SC-EGFRvIII-XG1-342 >1:64 >1:64

The secretion ELISA tests were performed as follows. For Ab secretion, 2μg/mL of Goat anti-human IgG H+L and for antigen binding, 1.5 μg/ml ofEGFRvIII-Rab Ig Fc fusion protein was coated onto Costar LabcoatUniversal Binding Polystyrene 96 well plates and held overnight at fourdegrees. The plates were washed five times with dH₂O. Recombinantantibodies were titrated 1:2 for 7 wells from the undilutedminilipofection supernatant. The plates were washed five times withdH₂O. A goat anti-human IgG Fc-specific HRP-conjugated antibody wasadded at a final concentration of 1 μg/mL for 1 hour at RT for thesecretion plates and binding plates detected with 1 μg/ml Rb anti Hu Fcfor 1 hour at room temperature. The plates were washed five times withdH₂O. The plates were developed with the addition of TMB for 30 minutesand the ELISA was stopped by the addition of 1 M phosphoric acid. EachELISA plate was analyzed to determine the optical density of each wellat 450 nm.

Sequencing and Sequence Analysis

The cloned heavy and light chain cDNAs were sequenced in both directionsand analyzed to determine the germline sequence derivation of theantibodies and identify changes from germline sequence. Such sequencesare provided in FIGS. 3A-3K and (SEQ ID NO: 34-55). A comparison of eachof the heavy and light chain sequences and the germline sequences fromwhich they are derived is provided in FIGS. 4-7. In addition, thesequence of the hybridoma derived 13.1.2 antibody is compared to itsgermline sequence in FIGS. 4 and 5.

As will be appreciated from the discussion herein, each of the 131antibody and the 13.1.2 antibody possess very high affinities forEGFRvIII, are internalized well by cells, and appear highly effective incell killing when conjugated to toxins. Intriguingly, each of theantibodies, despite having been generated in different immunizations ofXenoMouse mice, and utilizing different technologies, each are derivedfrom very similar germline genes. Based upon epitope mapping work(described herein), each of the antibodies, however, appear to bind toslightly different epitopes on the EGFRvIII molecule and have slightlydifferent residues on EGFRvIII that are essential for binding. Theseresults indicate that the germline gene utilization is of importance togeneration of antibody therapeutics targeting EGFRvIII and that smallchanges can modify the binding and effects of the antibody in ways thatallow further design of antibody and other therapeutics based upon thesestructural findings.

Binding of Anti-EGFRvIII mAbs to Native EGFRvIII Expressed on Cells

In this example, binding of anti-EGFRvIII antibodies to NR6 M cells wasmeasured. Specifically, unquantitated supernatants of XenoMax derivedIgG1 recombinant antibodies were assayed for their ability to bind toNR6 M and NR6 WT cells. Cells were seeded at 10000/well and incubatedovernight at 37 C in FMAT 96 well plates. Media was removed and 40 μlmini lipo supernatant (titrated down) was added, the cells wereincubated on ice for 1 hr. The human 13.1.2 EGFRvIII antibodies and ABXEGF (E7.6.3, U.S. Pat. No. 6,235,883) antibodies were added as positivecontrols. The PK 16.3.1 antibody was used as a negative control. Thecells were washed with Cold PBS, secondary antibody was added (SS Alexaantihuman IgG Fc) at 1 μg/ml, 40 μl/well and incubated on ice for 1 hr.The cells were then washed with Cold PBS and fixed and read by FMAT. Allantibodies were tested for specificity for binding by counter screeningagainst NR6 WT cells.

Purification of Recombinant Anti-EGFRvIII Antibodies

For larger scale production, heavy and light chain expression vectors(2.5 μg of each chain/dish) were lipofected into ten 100 mm dishes thatwere 70% confluent with HEK 293 cells. The transfected cells wereincubated at 37° C. for 4 days, the supernatant (6 mL) was harvested andreplaced with 6 mL of fresh media. At day 7, the supernatant was removedand pooled with the initial harvest (120 mL total from 10 plates). Eachantibody was purified from the supernatant using a Protein-A Sepharose(Amersham Biosciences, Piscataway, N.J.) affinity chromatography (1 mL).The antibody was eluted from the Protein-A column with 500 mcL of 0.1 MGlycine pH 2.5. The eluate was dialyzed in PBS, pH 7.4 andfilter-sterilized. The antibody was analyzed by non-reducing SDS-PAGE toassess purity and yield. Concentration was also measured by UV analysisat OD 250.

Internalization of EGFRvIII Receptor by Recombinant Anti-EGFRvIII mAbs

XenoMax derived IgG1 recombinant antibodies were expressed, purified andquantitated as described previously. Antibodies were further assayed fortheir ability to internalize the EGFRvIII receptor in NR6 M cells.250,000 NR6 M cells were incubated with primary antibody (SC95, SC131,SC133, SC139, SC150, SC170, SC211, SC230, SC250 and human. 13.1.2 as acontrol) at 0.25 μg/ml, 7 mins on ice in 96 well v-bottomed plate intriplicate. The cells were washed with cold 10% FCS in PBS and secondaryantibody (SS Alexa antihuman IgG Fab) at 3 μg/ml Fab was added andincubated for 7 mins on ice. The cells were washed with cold 10% FCS inPBS once and then resuspended in cold media. Next, two sets of thetriplicate were incubated at 37° C. and the remaining set was incubatedat 4° C. for 1 hr. After that the cells incubated at 4° C. and one setof the cells incubated at 37° C. were treated with glutathione (aspreviously mentioned) for 1 hr on ice. Then the cells were washed andresuspended in 100 μl of cold 1% FCS in PBS and analyzed by FACS. The %internalization was calculated from the geometric mean obtained from theFACS analysis [(mean at 37° C. with glutathione−mean at 4° C. withglutathione)/(mean at 37° C. without glutathione−mean at 4 C withglutathione)]. NA means that a FACS analysis was performed but the datawas not provided in Table 3.12.

TABLE 3.12 FACS Geometric mean Without With glutathione glutathione Withglutathione % mAb 37° C. 37° C. 4° C. internalization 13.1.2 22.12 19.195.38 82.5% sc95 22.56 17.75 5.13 72.4% sc131 NA NA NA   72% sc133 23.3918.63 6.24 72.2% sc139 22.64 19.23 4.88 80.8% sc150 20.29 7.78 4.6620.0% sc170 19.97 7.75 4.67 20.1% sc211 20.76 8.23 4.78 21.6% sc23020.68 7.97 5.02 18.8% sc250 24.13 8.07 4.84 16.7%

13.1.2 is an antibody that was generated through hybridoma generation(Example 2) that was directed against the EGFRvIII epitope previouslyand was used as a positive control in this experiment. These results inTable 3.12 demonstrate the presence of two subsets of antibodies, thosethat are efficiently internalized (70-80%) and those that are not (22%or less).

Example 4 Epitope Mapping of Human Anti EGFRvIII Antibodies

In order to determine the epitopes to which certain of the antibodies ofthe present invention bound, the epitopes of 6 human and 3 murinemonoclonal antibodies (mabs) against EGFRvIII were mapped usingsynthetic peptides derived from the specific EGFRvIII peptide sequence.The antibodies mapped were the human hybridoma derived anti-EGFRvIII13.1.2 antibody, the human XenoMax derived anti-EGFRvIII 131, 139, 250,095, and 211 antibodies and the murine anti-EGFRvIII H10, Y10, and B9antibodies (from Dr. D. Bigner, Duke University).

The approach that was used was a custom SPOTs peptide array (SigmaGenosys) to study the molecular interaction of the human anti-EGFrVIIIantibodies with their peptide epitope. SPOTs technology is based on thesolid-phase synthesis of peptides in a format suitable for thesystematic analysis of antibody epitopes. Synthesis of custom arrayedoligopeptides is commerically available from Sigma-Genosys. A peptidearray of overlapping oligopeptides derived from the amino-acid sequenceof the EGFr VIII variant was ordered from Sigma-Genosys.

A series of nine 12-mer peptides were synthesized as spots onpolypropylene membrane sheets. The peptide array spanned residues 1-20of the EGFrVIII sequence, representing the deletion of amino acids 6-273in the extracellular domain of wtEGFr, and the generation of a glycine(G) residue at the junction point. Each consecutive peptide was offsetby 1 residue from the previous one, yielding a nested, overlappinglibrary of arrayed oligopeptides. The membrane carrying the 9 peptideswas reacted with 9 different anti EGFrVIII antibodies (1 μg/ml). Thebinding of the mAbs to the membrane-bound peptides was assessed by anenzyme-linked immunosorbent assay using HRP-conjugated secondaryantibody followed by enhanced chemiluminescence (ECL). The arrayutilized is shown in Table 4.1.

TABLE 4.1 Spot Array Sequence: 1. ALEEKKGNYVVT (SEQ ID NO: 72)2. LEEKKGNYVVTD (SEQ ID NO: 59) 3. EEKKGNYVVTDH (SEQ ID NO: 73)4. EKKGNYVVTDHG (SEQ ID NO: 74) 5. KKGNYVVTDHGS (SEQ ID NO: 75)6. KGNYVVTDHGSC (SEQ ID NO: 76) 7. GNYVVTDHGSCV (SEQ ID NO: 77)8. NYVVTDHGSCVR (SEQ ID NO: 78) 9. YVVTDHGSCVRA (SEQ ID NO: 79)

In addition, functional epitopes were mapped by combinatorial Alaninescanning. In this process, a combinatorial Alanine-scanning strategy wasused to identify amino acids in the EGFrVIII peptide necessary forinteraction with anti-EGFRvIII mAbs. To accomplish this, a second set ofSPOTs arrays was ordered for Alanine scanning. A panel of variantspeptides with alanine substitutions in each of the 12 residues wasscanned as above. Spot #1, the unmutated sequence, is a positive controlfor antibody binding. The array utilized is shown in Table 4.2.

TABLE 4.2 Alanine Scanning Array:   1. LEEKKGNYVVTD (SEQ ID NO: -59) 2. AEEKKGNYVVTD (SEQ ID NO: 80)  3. LAEKKGNYVVTD (SEQ ID NO: 81) 4. LEAKKGNYVVTD (SEQ ID NO: 82)  5. LEEAKGNYVVTD (SEQ ID NO: 83) 6. LEEKAGNYVVTD (SEQ ID NO: 84)  7. LEEKKANYVVTD (SEQ ID NO: 85) 8. LEEKKGAYVVTD (SEQ ID NO: 86)  9. LEEKKGNAVVTD (SEQ ID NO: 87)10. LEEKKGNYAVTD (SEQ ID NO: 88) 11. LEEKKGNYVATD (SEQ ID NO: 89)12. LEEKKGNYVVAD (SEQ ID NO: 90) 13. LEEKKGNYVVTA (SEQ ID NO: 91)

Epitopes of all 9 mAbs to the human EGFrVIII were mapped and identifiedby SPOTs procedure. All 9 antibodies were reactive with the peptides.The results obtained with 3 murine antibodies and 6 XenoMouse mousederived human antibodies are presented in Table 4.3. Highlightedresidues are those which we mutated to alanine and abrogated binding bythe test antibody. These are therefore relevant residues for binding tothe antibody.

TABLE 4.3 EGFR A T C V K K C P R N Y V V T D H G S C V R A SEQ ID NO: 92EGFRvIII L E E K K G N Y V V T D H G S C V R A (SEQ ID NO: 93) 13.1.2 EE K K G N Y V V T (SEQ ID NO: 94) 131 E E K K G N Y V V T (SEQ IDNO: 94) 139 L E E K K G N Y V V T D (SEQ ID NO: 95) 250 L E E K K G N YV V T D (SEQ ID NO: 95) 095 Y V V T D H (SEQ ID NO: 96) 211 Y V V T D(SEQ ID NO: 97) H10 Y V V T D (SEQ ID NO: 97) Y10 E E K K G N Y V V T(SEQ ID NO: 98) B9 G N Y V V T (SEQ ID NO: 99)

The shaded amino acids shown in Table 4.3 are the most relevant residuesin the eiptope for antibody recognition. The minimal lengths of epitopesof all ten of the mAbs were precisely mapped using peptides ofoverlapping sequences, and the tolerance for mAb binding to mutatedepitopes was determined by systematically replacing each residue in theepitope with Alanine.

In Table 4.4, additional characteristics of the antibodies aresummarized. Specifically, a subset of the antibodies were tested fortheir binding of to lysates of tumor cell lines in Western plates ofpolyacrylamide gel electrophoresis under either non-reducing or reducingconditions. Purified recombinant protein is also included. Antibodiesbinding in both reducing and non-reducing conditions suggest that theepitope is linear. Sample identifications:

EGFRvIII—the rabbit Fc fusion protein

H1477—H80 human tumor cell line transfected with EGFRvIII expressionconduct. These cells express both EGFR and EGFRvIII.

EGFR purified wild-type EGFR protein

A431—human tumor cell line expressing only wild-type EGFR

A549—human tumor cell line expressing only wild-type EGFR

H80—human tumor cell line expressing only wild-type EGFR

EGFR Biacore—mAbs were tested in Biacore for binding to purifed EGFR asa highly sensitive test for specificity

TABLE 4.4 EGFRvIII rEGFRvIII H1477 H1477 EGFR EGFR Western WesternEGFRvIII Western Western pep3 Western Western mAb (native) (reduced)FACS (native) (reduced) KinExA (native) (reduced) 13.1.2 + + + + + 25 pM− − 131 + + + + + 0.05 pM − − 139 ? + + ND ND ND ND ND 095 + + + ND NDND ND ND 211 + + + ND ND ND ND ND 250 + + + ND ND ND ND ND A431 A431A549 A549 H80 H80 EGFR A431 Western Western A549 Western Western H80Western Western MAb Biacore FACS (native) (reduced) FACS (native)(reduced) FACS (native) (reduced) 13.1.2 − − − − − − − − − − 131 − ++ −− + − − − − − 139 N.D. ND ND ND ND ND ND ND ND ND 095 − ND ND ND ND NDND ND ND ND 211 − ND ND ND ND ND ND ND ND ND 250 − ND ND ND ND ND ND NDND ND

The results showed that most of these mAbs have essentially the samebinding specificity, seven of the mAbs were shown to bind specificallyto the EGFrVIII variant, while 2 mAbs cross reacted with wildtype EGFr(murine H10 and human 211) in Western blots of purified protein and inlysate of A431 cells. Note, however, that while antibody 211 binds toboth native and reduced purified EGFRvIII in Western blots, it bindsslightly more strongly to the non-reduced protein. In tests against alysate of A431 cells, antibody 211 binds strongly to a band of the sizeof wild-type EGFR in the non-reduced sample but there is no signal inthe reduced sample. This suggests that the binding of antibody 211 isdue to a conformational epitope present in wild-type EGFR andrepresented differently in the EGFRvIII variant. The epitopes of 5 ofthe mAbs are within residues 2-12 spanning the EGFRvIII variant specificGlycine residue, whereas the epitope of 4 of the mAbs (including H10 and211) spans residues 7-16 which are common to the EGFRvIII and wildtypeEGFr. Antibody 131 binds to A431 and A549 cells in FACS. These cells areapparently negative for expression of EGFRvIII while positive for EGFRexpression. Antibody 131 does not bind to non-reduced or non-reducedpurified EGFR or to reduced or non-reduced lysates of A43 and A549 cellsin Westerns suggesting that antibody 131 may be binding to a variant ofEGFR expressed on the cell surface of some human tumor cell lines. Thisvariant would be sensitive to denaturation.

Example 5 Characterization of Specificity of Anti-EGFRvIII Antibodies InVitro

The specificity of the purified antibodies was ascertained by performingFACS analysis on NR6 cells that were transfected with either wild typeor mutant EGFR. Cells were incubated on ice with 5 μg/ml of therespective antibody for 1 hr, washed in FACs buffer and subsequentlyincubated with PE-conjugated goat anti-human IgG.

Example 6 Cross-Reactivity with Amplified EGFR

Antibodies directed to variant EGF receptors have been shown tocross-react with subsets of wild type EGF receptors on cells in whichgene amplification has occurred (Johns et al., Int. J. Cancer. 98: 398,2002). To determine whether the human EGFRvIII antibodies identified hadsimilar properties, they were tested for their ability to recognize wildtype EGF receptors on a variety of cells in culture. Antibodies wereincubated with the indicated cell lines at 4° C. After washing in FACSbuffer, a secondary antibody conjugated with phyoerythrin was added andthe incubation was continued. All cell lines analyzed expressed wildtype EGFR. A subset of wild type EGFRs was recognized by the antibodyXG1-131 on both A431 and SF-539 cells but not on A498 or SKRC-52 cells.Another antibody to EGFRvIII, 13.1.2, did not recognize this subset ofwild type EGFRs. When considered together these data indicate that onlya subset of antibodies directed to the mutant EGFRvIII are able torecognize wild type EGFRs on the surface of cells. The ability ofcertain antibodies directed to mutant EGFRvIII to recognize asubpopulation of wild type EGF receptors is not dependent on total EGFRdensity but likely represents a novel conformational epitope that isunique to tumor cells. The ability of antibodies directed to EGFRvIII tocross-react with subpopulations of wild type receptors may be determinedby both the specific epitope within the junction of the mutant receptorand the affinity of the antibody for this unique epitope (See theresults of the epitope mapping and affinity determination sectionherein).

Example 7 Characterization of Specificity of Anti-EGFRvIII Antibodies InVitro: Binding of the Antibodies to Cell Lines

The specificity of the purified antibodies was ascertained by performingFACS analysis on a panel of cell lines. H80, a human glioblastoma line,and H1477 (H80-EGFRvIII) that expresses high levels of EGFRvIII, A431, ahuman epidermoid carcinoma line, and A549, a human lung carcinoma cellline were used as the cell lines. All cell lines were from. Dr. Bignerexcept A431 and A549, which were from ATCC (Rockville, U.S.A.). Cellswere incubated on ice with 10 μg/ml of the respective antibody for 30washed in FACS buffer and subsequently incubated with PE-conjugated goatanti-human IgG from Jackson ImmunoResearch (West Grove, Pa., U.S.A.). InFIGS. 9A-9L and 10A 10D, the darkened histogram indicates cells stainedwith an irrelevant IgG, the outlined, or white histogram, represents thestaining of the relevant antibodies. The anti-EGFRvIII antibodies13.1.2, 131 and 139 bind to the EGFRvIII protein on the transfected celllines. A graph summarizing some of the results is displayed in FIGS.9M-9P.

Antibodies directed to variant EGF receptors have been shown tocross-react with subsets of wild type EGF receptors on cells in whichgene amplification has occurred (Johns et al., Int. J. Cancer. 98: 398,2002). In this example, A431 and A549 stained by XG1-131 and XG1-139.FIG. 10B and FIG. 10 C show that 131 and 139 have certain crossreactivity with the wild type EGFR instead of just recognizing a subsetof population in H80, A431 and A549 line. However, this cross reactivityis only at 10% of the level of ABX-EGF (E7.6.3) staining on these celllines. The results are provided in FIGS. 9A-9P and 10A-10D.

Antibodies directed to cell surface antigens can be used as deliveryvehicles that specifically transport drugs or toxins into cells. If theantibody stimulates internalization of antigen, the drug or toxin canresult in death of the cell, perhaps after the drug or toxin is cleavedfrom the antibody. Such a mechanism can he utilized to specifically killtumor cells in animals and in patients. One way to select antibodiesthat can deliver drugs to cells is through secondary cytotoxicityassays. In these assays the primary antibody binds to the cell surfaceand a secondary antibody that is conjugated with a drug or toxin isadded. If the primary antibody stimulates antigen internalization, thesecondary antibody will be co-internalized and upon cleavage of the drugor toxin result in cell killing.

Example 8 Secondary Cytotoxicity Assays

This example demonstrates how the antibodies could be used to directtoxins conjugated via secondary antibodies to cells expressing thetarget epitope (target cell). Antibodies conjugated to a toxin areadministered to cells expressing the target peptide. The death of thosecells indicates the effectiveness of the antibody toxin combination.

The amount of specific killing required can vary depending upon theparticular use. In one embodiment, any reduction in possibly cancerouscells is sufficient. For example, a reduction of 0-1, 1-5, 5-10, 10-20,20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-95, 95-99, or 100%of the target cells will be sufficient. In another embodiment, thedesired reduction in target cell number is also a function of thenonspecific lethality of the antibody combination. For example,antibody/toxin combinations that only have a 10% decrease in target cellnumber may be sufficient, if there is very little nonspecific targetingand lethality by the antibody. For example, the antibody toxincombination kills less than 10% of a non-target population. Again, theparticular amount will depend on the particular need and situation.Particularly useful are antibodies that are highly selective for atarget cell and bind well to the target cell, or proteins associatedwith the cell. In one embodiment, the target is the EGFRvIII protein, ora fragment thereof. In one embodiment, antibodies that are human, orhumanized, efficient at being internalized, specific to the EGFRvIIIprotein or fragments thereof, associate tightly with the EGFRvIIIprotein or fragment, and are associated with an effective toxin, aretaught from these examples.

Example 9 Secondary Cytotoxicity Clonogenic Assays

In addition to the secondary Cytotoxicity assays, EGFRvIII-specificantibodies can also be used for clonogenic assays. As above, antibodiesassociated with toxin are administered to cells. The ability of thecells to proliferate is monitored. A decrease in proliferation indicatesthat the antibody toxin combination is effective.

Example 10 Anti-EGFRvIII Antibody (13.1.2) Direct Conjugates in theCytotoxicity Assays

In addition to the indirectly conjugated examples above, these tests canalso be performed with antibodies that are directly conjugated to thetoxins. An antibody that is directly conjugated to a toxin is used inthe same manner as described for the antibody toxin conjugate in Example8.

Example 11 In Vivo Anti-EGFRvIII Antibodies Characterization

The antibody toxin conjugates can also be tested in vivo. An antibodytoxin conjugate is administered to a test organism that has target cellsthat are expressing the target peptide. A decrease in the number oftarget cells in the test organism indicates the ability of the antibodyconjugated toxin to work in an in vivo setting.

Example 12 Expression of EGFRvIII in Cancer Patients/Human Tumors

The expression of EGFRvIII on human tumors was determined by stainingfrozen tissue sections from a variety of cancer patients with acombination of 2 murine monoclonal antibodies (B9, IgG1 and Y10, IgG2(Dr. Bigner, Duke University)) known to bind specifically to EGFRvIII.The same sections were stained with isotype matched control antibodies.A summary of the staining results obtained from all patient samples ispresented in Table 12.1.

TABLE 12.1 Summary Of Staining Results From Patient Samples Tumor typeSample Size (N) EGFRvIII > + EGFRvIII > ++ Glioblastoma 8 100% 100%Breast Cancer 100  31%  24% NSCL cancer 51  47%  39% Head & neck Cancer21  42%  38% Prostate Cancer 22   4.5%   4.5% EGFRvIII > +: include alltumors that express EGFRvIII EGFRvIII > ++: include only those tumorsthat express at least 10% or more EGFRvIII

The expression was found primarily on the cell membrane and/orcytoplasm. Significant numbers of breast (31%), NSCL (47%), and head &neck (42%) cancer specimens stained positively for EGFRvIII. In certaininstances, in order to obtain high quality IHC staining, the use of twoantibodies can be better than the use of one antibody. Frozen tissuespecimens were superior over fixed tissues.

As appreciated by one of skill in the art, it may be advantageous totest patients before using therapeutic antibodies to ensure that thetumor which is being treated expresses EGFRvIII.

Example 13 In Vivo Anti-EGFRvIII Antibodies Characterization

The method of Example 11 will be used to treat lung cancer and gliomas.This will be broadly examined by producing animal models. Animal modelsfor glioblastoma and lung cancer are developed as follows: lung cancercells that express wt-EGFR are transfected with EGFRvIII. The cells areinjected into the lungs of nu/nu mice and tumors allowed to progress toa comparable stage to that above. Anti-EGFRvIII conjugates will then beinjected intravenously as above every 1 to 10 days as needed. The sizeand prevention or suppression of continued growth of these cancer cellswill then be monitored, to determine the effectiveness of theseAnti-EGFRvIII antibodies and antibody-toxins combinations. Asappreciated by one of skill in the art, this can be done for any of theantibodies disclosed herein.

Example 14 Functional Characterization of Epitopes by SubstitionalAnalyses

In order to further resolve the identity of those amino acid residuesthat are indispensable for binding within the EGFRvIII epitope,substitutional analyses of the amino acids in the epitope peptides wereperformed. The starting point was the sequence that was derived fromExample 4, LEEKKGNYVVTD (SEQ ID NO 59). In this example each amino acidof the mapped epitope was substituted one-at-a-time by all 20 L-aminoacids, thus, all possible single site substitution analogs weresynthesized and screened to provide detailed information on the mode ofpeptide binding. Discrete substitution patterns were identified for mAbs131 and 13.1.2. The results from the substitutions are summarized inTable 14.1.

TABLE 14.1  mAbs Recognition sequence 131 EEKKGNYVVT (SEQ ID NO: 57)13.1.2 EEKKGNYVVT (SEQ ID NO: 57)

It appears that for mAb 13.1.2, 5 residues are important for binding(bold), while only 4 residues are essential for the binding of mAb 131.The rest of the residues were replaced by various amino acids withoutsignificant loss of binding. Although the 131 and 13.1.2 epitopes areidentical by sequence and length, the binding pattern for each appearsdifferent. Binding of mAb 131 is strongly dependent on the residues EKNY(SEQ ID NO: 60). On the other hand, the data revealed that residuesEEKGN (SEQ ID NO: 61) are involed in binding of mAb 13.1.2.

Example 15 mABS Chain Shuffling

Heavy and light chains of mAbs 131 and 13.1.2 were shuffled andtransiently transfected into 293T cells. Seventy-two hours latersupernatants were collected and assayed for secretion and binding toEGFrVIII antigen by ELISA.

The results demonstrated that antibodies derived from expression of 131heavy chain with 13.1.2 kappa chain, and vice versa were expressed wellbut binding activity was reduced by 75% probably due to the differentbinding pattern of these two mAbs to EGFrVIII antigen. (data not shown).This demonstrates the difference between the two paratopes of the 131and 13.1.2 mAbs, again suggesting that the structural characteristics ofthe epitope selected for between the two mAbs are different.

Example 16 Molecular Modeling of 131 and its Paratope

This example demonstrates how three-dimensional structures can begenerated for the proteins of the embodiments. The three-dimensionalstructure model of the variable region of antibody 131 was generatedthrough a homology modeling approach using the InsightII modelingpackage from Accelrys (San Diego, Calif.). The model was built from thevariable region sequences described below, Table 16.1. The residuenumbering starts with the light chain amino acids, and continues toheavy chain amino acids.

TABLE 16.1 Light chain variable region DTVMTQTPLSSHVTLGQPASISC(SEQ ID NO: 100) RSSQSLVHSDGNTYLS (CDR1) (SEQ ID NO: 101) WLQQRPGPPRLLIY(SEQ ID NO: 102) RISRRFS (CDR2) (SEQ ID NO: 103)GVPDRFSGSGAGTDFTLEISRVEAEDVGVYYC (SEQ ID NO: 104) MQSTHVPWT (CDR3)(SEQ ID NO: 105) FGQTKVEIK (SEQ ID NO: 106) Heavy chain variable regionQVQLVESGGGVVQSGRSLRLSCAASGFTFR (SEQ ID NO: 107) NYGMH (CDR1)(SEQ ID NO: 108) WVRQAPGKGLEWVA (SEQ ID NO: 109)VIWYDGSDKYYADSVRG (CDR2) (SEQ ID NO: 110)RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAR (SEQ ID NO: 111)DGYDILTGNPRDFDY (CDR 3) (SEQ ID NO: 112) WGQGTLVTVSS (SEQ ID NO: 113)

Antibody 131 sequences were used to search against the Protein Data Bankto identify homologous antibodies and their structures. Based on thehomologous antibodies' sequence similarity to the 131 antibody, severalstructures were selected. The structures selected for modeling samplesfrom the Protein Data Bank had the Protein Data, Bank identifications of1HEZ, 2H1P, 1 AQK, 1DQL, 1MF2 and 1FLR. These template structures werethen aligned by superposition and used to generate structure-basedsequence alignments among the templates. The sequences of antibody 131'svariable region were then aligned to the template sequences. Thestructure and sequence alignments were used to generate the molecularmodel for the variable region of the 131 antibody. The sequence forCDR1, light chain was: RSSQSLVHSDGNTYLS (SEQ ID NO 103). The sequencefor CDR2, light chain was: RISRRFS (SEQ ID NO 103). The sequence forCDR3, light chain was: MQSTHVPWT (SEQ ID NO 105). The sequence for CDR1,heavy chain was: NYGMH (SEQ ID NO 108). The sequence for CDR2, heavychain was: VIWYDGSDKYYADSVRG (SEQ ID NO 110). The sequence for CDR3,heavy chain was: DGYDILTGNPRDFDY (SEQ ID NO 112).

The interaction surface for antibody 131 was calculated from thestructure model and shown in FIG. 11. The various CDRs are identified asfollows: L1 (light CDR1) 10, H1 (heavy CDR1) 20, L2 30, H2 40, L3 50 andH3 60. A prominent feature on the predicted antibody 131 interactionsurface is a deep cavity. The cavity is mainly surrounded by heavy chainCDR2, CDR3 and light chain CDR3, with a small portion contributed bylight chain CDR1. The cavity is probably the binding pocket. Within 5Angstroms of the binding cavity are residues 31, 37, 95-101, 143-147,159, 162-166, 169-171, 211-219, 221 and 223. These residues are likelyto comprise the paratope and make key contacts in the binding ofEGFRvIII epitope. It is also likely that the residues provide importantstructural features to the binding site in general.

Example 17 Site-Directed Mutagenesis Confirming the Model for Antibody131

This example demonstrates one method by which models that suggestresidues that are important in binding may be tested. The Example alsoresults in several antibody variants. Antibody variants of the 131 clonewere generated by single residue mutations introduced to the heavy andthe light chain of mAb 131. These variants were then analyzed todetermine how the altered side chains from the point mutationcontributed to antigen binding.

Changes were made in the heavy and light chains of mAb 131. On the heavychain L216 was changed by site directed mutagenesis to R. On the lightchain, V99 was changed to F. Both mutations affected the expression andsecretion of the variant antibodies compared to the wildtype sequence.Both mutations resulted in a loss of binding of the mAb variant to theEGFRvIII antigen. This demonstrates L216 and V99 probably havesignificant contacts with the EGFRvIII antigen since substitutions ofthese residues to R and F respectively resulted in reduced activity. Ofcourse, it is always an option that these substitutions are disruptiveto the antibody's general structure.

Example 18 Molecular Modeling of 13.1.2 and its Paratope

The three-dimensional structure model of the variable region of the13.1.2 antibody was generated through homology modeling approach withthe InsightII modeling package from Acceirys (San Diego, Calif.). Themodel was built from the variable region sequences, shown below in Table18.1, using the published x-ray crystal structures as templates.

TABLE 18.1  Light chain variable region (1-113) DIVMTQTPLSSPVTLGQPASISC(SEQ ID NO: 114) RSSQSLVHSDGNTYLS (CDR1) (SEQ ID NO: 101)WLHQRPGQPPRLLIY (SEQ ID NO: 115) KISNRFS (CDR2) (SEQ ID NO: 116)GVPDRFSGSGAGTAFTLKISRVEAEDVGVYYC (SEQ ID NO: 117) MQATQLPRT (CDR3)(SEQ ID NO: 118) FGQGTKVEIKR (SEQ ID NO: 119)Heavy chain variable region (114-234)  QVQLVESGGGVVQPGRSLRLSCAASGFTFS(SEQ ID NO: 120) SYGMH (CDR1) (SEQ ID NO: 121) WVRQAPGKGLEWVA(SEQ ID NO: 122) VIWYDGSNKYYVDSVKG (CDR2) (SEQ ID NO: 123)RFTISRDNSKNTLYLQMNSLRAEDTAVYYCAR (SEQ ID NO: 124) DGWQQLAPFDY (CDR3)(SEQ ID NO: 125) WGQGTLVTVSSA (SEQ ID NO: 126)

The sequence for CDR1, light chain was: RSSQSLVHSDGNTYLS (SEQ ID NO:101). The sequence for CDR2, light chain was: KISNRFS (SEQ ID NO: 116).The sequence for CDR3, light chain was: MQATQLPRT (SEQ ID NO: 118). Thesequence for CDR1, heavy chain was: SYGMH (SEQ ID NO: 121). The sequencefor CDR2, heavy chain was: VIWYDGSNKYYVDSVKG (SEQ ID NO: 123). Thesequence for CDR3, heavy chain was: DGWQQLAPFDY (SEQ ID NO: 125).

Antibody 13.1.2 sequences were used to search the Protein Data Bank toidentify homologous antibodies. The structures with the Protein DataBank identifications of 1HEZ, 2H1P, 8FAB and 1AQK were selected asmodeling templates, based on their sequence similarity to antibody13.1.2. The template structures were aligned by superposition and usedto generate structure-based sequence alignments among the templates. Thesequences of the variable regions of the 13.1.2 antibody were thenaligned to the template sequences. The structure and sequence alignmentswere used to generate the molecular model for antibody 13.1.2 variableregion.

The interaction surface was calculated for the model and is shown inFIG. 12. A major feature of the 13.1.2 model is a long and narrow grooveon the surface of the CDR region. The groove is outlined by heavy chainCDR2 140, CDR3 160, and light chain CDR1 110, CDR2 130 and CDR3 150. Oneend of the groove touches the rest of light chain CDR3 150, and theother end opens to the wider area of heavy chain CDR3 160 near the heavychain-light chain interface. The groove is probably the binding pocketfor the antigen. Within 5 Angstroms of the binding groove are residues31, 33, 35-39, 51, 54-56, 58-61, 94-101, 144-148, 160, 163-166, 172, and211-221. These residues are likely to comprise the paratope for thebinding of EGFRvIII epitope. It is also likely that the residues provideimportant structural features to the binding site in general.

Example 19 Docking Models of a Peptide to an Antibody

The epitope mapping studies in Example 14 revealed that the relevantamino acids required for binding of the epitope to the paratope of13.2.1 mAb reside in the six-residue peptide EEKKGN (SEQ ID NO: 127).Therefore, docking models of this six-residue peptide complexed to theCDR region of 13.1.2 structure model were generated. First, a model ofthe peptide EEKKGN (SEQ ID NO: 127) was produced. This was done,similarly as described before, except this time using the x-ray crystalstructure of 1181, as identified in the Protein Data Bank, as thetemplate. Next, this peptide structure was manually placed into the longgroove to form an initial assembly complex. A Monte Carlo search in theconformational and orientational spaces were then automaticallyperformed with the Docking module in InsightII. The peptide conformationwas allowed to be flexible by giving each of the Phi, Psi and Chi anglesfull rotational freedom. During the docking process, the residues within5 Angstroms of the binding groove were allowed to move while the otherresidues of the antibody were fixed. The plausible configurations foundby Monte Carlo search were subjected to simulated annealing and energyminimization to reach the final complex structure models. For eachdocking model obtained, the interaction energy between the antibody andthe peptide was calculated with the Discover_3 module of InsightIIpackage. The interaction energies for all docking models were assessedand the model with the strongest overall antibody-peptide interactionwas examined and is shown in FIGS. 13A and 13B.

In this docking model, there are six hydrogen bonds between peptideEEKKGN (SEQ ID NO: 127) and antibody 13.1.2, as shown in FIG. 13B. Thepeptide residue number is labeled from N-terminus to the C-terminus as 1through 6. Six hydrogen bonds are indicated by green dashed lines. Thesix pairs of amino acids forming hydrogen bonds are: E2 . . . Y172, K3 .. . H31, K4 . . . H31, N6 . . . D33, N6 . . . Y37, and N6 . . . K55. Inthis docking model, the peptide is bound to the groove in an extendedβ-strand conformation. Residues in the peptide alternately face thesolvent and the antibody surface. The residues facing the binding groovewith the most significant contacts to the antibody are E2, K4 and N6.This indicates that these three residues may be important to peptidebinding, consistent with the epitope mapping results. The interactionenergies for each of the six peptide residues with the 13.1.2 paratopewas calculated with the Discover_3 module and the results are shown inTable 19.1. Table 19.1 shows the interaction energies for each of thesix peptide residues with the 13.1.2 paratope. All energies are in theunit of kcal/mol.

The residues with the strongest interaction energies are in the order ofN6, K4 and E2, confirming that these residues are key contributors onthe antigen side in the antibody-antigen interaction, again consistentwith experimental data. These data provided strong evidence to supportthe docking model. In this embodiment, the paratope is defined as theresidues within 5 Angstroms of the docked peptide. The 20 residuescomprising the paratope as so defined are residues 31-33, 35, 37, 55,96-101, 148, 163, 165, 170, 172, 178 and 217-218. To evaluate, on anindividual residue basis, the contribution of each of these residues ofthe antibody in the antibody-antigen interaction, the interaction energybetween the paratope residues and the peptide EEKKGN (SEQ ID NO: 127)was calculated for each of the above 20 residues. The results are listedin Table 19.2. Table 19.2 shows the interaction energies for each of the20 paratope residues with the peptide EEKKGN (SEQ ID NO:127). Allenergies are in the unit of kcal/mol. The residues with the strongestinteraction energies with the peptide are Lys55 and His31, followed byTyr172, Ala96, Asp33, Tyr37, Leu99, Thr97, Gln98, Lys178 and Asn170.

TABLE 19.1 Peptide Residue Coulumbic VdW Total E1 −2.013 −3.738 −5.751E2 −10.661 −0.617 −11.278 K3 −9.816 −0.493 −10.309 K4 −11.123 −0.968−12.091 G5 −1.241 −1.468 −2.709 N6 −16.504 −0.181 −16.685

TABLE 19.2 13.1.2 Residue Coulumbic VdW Total His31 −12.835 3.033 −9.801Ser32 2.857 −1.062 1.794 Asp33 −4.181 −0.698 −4.879 Asn35 0.253 −1.009−0.756 Tyr37 −2.058 −2.463 −4.521 Lys55 −14.363 1.568 −12.794 Ala96−6.077 0.896 −5.182 Thr97 −2.739 −1.431 −4.171 Gln98 −2.542 −1.548 −4.09Leu99 −1.507 −2.779 −4.286 Pro100 0.439 −0.379 0.061 Arg101 3.992 −0.5493.443 His148 0.101 −0.083 0.018 Val163 −0.104 −0.237 −0.342 Trp165 1.358−1.122 0.236 Asn170 −2.102 −0.487 −2.589 Tyr172 −8.7 0.896 −7.804 Lys178−3.614 −0.03 −3.644 Leu217 0.761 −1.426 −0.664 Ala218 −0.071 −0.281−0.352

Example 20 Rational Design for Affinity-Improved Antibodies

This Example demonstrates how the docking model can be used as the basisof rational design for affinity-improved antibodies by site-directedmutagenesis. Each of the 13.1.2 paratope residues was mutated to all 19other amino acids in silico, resulting in a total of 19×20 or 380virtual mutants. The mutation was done by residue replacement followedby 50 steps of energy minimization to account for any localconformational changes that could be induced by the side chain change.The interaction energy between the whole peptide and the whole paratopewas calculated for each mutant. Mutants with a total interaction energystronger than the wild type 13.1.2 could potentially have a higheraffinity for the peptide EEKKGN (SEQ ID NO: 127), and perhaps even thewhole EGFRvIII protein. These mutants mostly have stronger coulumbicinteractions than the wild type 13.1.2, but some of them have weaker vander Waals (VdW) interactions than the wild type antibody. Consideringthat in the wild type 13.1.2 antibody, the VdW interacting energy is−9.689 kcal/mol, mutants with VdW interaction energy weaker than −8.5kcal/mol were filtered out. The rest of the mutants that have stronger,total interaction energy, than the wild type 13.1.2 are listed in Table20.1. The wild type data are listed at the bottom for comparison. Allenergies are in the units of kcal/mol.

TABLE 20.1 Mutant Coulumbic VdW Total Tyr172Arg −93.004 −8.702 −101.706Leu99Glu −79.897 −8.506 −88.403 Arg101Glu −77.984 −8.833 −86.817Leu217Glu −75.124 −8.998 −84.123 Leu99Asn −73.337 −9.894 −83.231Leu99His −73.631 −9.008 −82.639 Arg101Asp −71.983 −9.877 −81.861Leu217GIn −70.263 −9.795 −80.058 Leu99Thr −69.882 −10.153 −80.035Gln98Glu −70.651 −9.257 −79.908 Leu217Asn −70.989 −8.769 −79.758Arg101Gln −69.432 −10.164 −79.596 Leu217Asp −69.934 −9.643 −79.578Asn35Gly −69.016 −10.191 −79.207 Tyt172His −69.312 −9.509 −78.820Val163Asn −68.841 −9.944 −78.784 Tyr172Asn −68.896 −9.871 −78.767Ala218Lys −70.024 −8.570 −78.594 Asn35Arg −68.989 −9.604 −78.593Trp165Lys −69.578 −8.766 −78.344 Trp165Arg −68.814 −9.216 −78.030Leu99Tyr −67.052 −10.464 −77.517 Tyr172Thr −68.146 −9.225 −77.371Ala96Thr −67.534 −9.623 −77.158 Ala96Ser −67.222 −9.822 −77.045Pro100Trp −67.399 −9.496 −76.894 Leu217Ser −66.676 −10.133 −76.810Ser32Ile −66.700 −10.077 −76.777 Tyr172Ser −67.588 −9.146 −76.734His31Glu −67.070 −9.461 −76.531 Leu217Tyr −65.605 −10.726 −76.331Val163His −67.236 −9.064 −76.300 His148Ser −66.780 −9.495 −76.274His148Val −66.634 −9.629 −76.263 His148Ala −66.770 −9.473 −76.243His148Gly −66.762 −9.456 −76.217 His148Thr −66.700 −9.508 −76.209Leu99Ser −66.126 −10.006 −76.132 Pro100Asp −66.153 −9.787 −75.940Trp165Glu −66.665 −9.267 −75.932 His148Asn −66.010 −9.889 −75.899Pro100Gln −65.873 −9.871 −75.745 Leu217Thr −66.045 −9.672 −75.717Ser32Val −65.845 −9.854 −75.699 Ser32Pro −65.807 −9.813 −75.620Pro100Gly −65.841 −9.774 −75.615 Pro100Ala −65.889 −9.712 −75.601Ser32Ala −65.497 −10.089 −75.586 Ser32Thr −65.723 −9.861 −75.584Ala218Thr −66.054 −9.505 −75.560 Pro100Ser −65.831 −9.699 −75.530Val163Gly −65.993 −9.536 −75.529 Gln98Thr −66.162 −9.277 −75.438Pro100Met −65.811 −9.602 −75.412 Ser32Met −66.252 −9.153 −75.406Ser32Gly −65.509 −9.891 −75.399 Pro100Asn −65.729 −9.655 −75.384Tyr37Phe −66.253 −9.020 −75.272 Val163Ala −65.713 −9.543 −75.255Leu217Ile −65.479 −9.759 −75.238 Wild type 13.1.2 −65.517 −9.689 −75.205

The mutants listed in Table 20.1 could be candidates for engineering ofaffinity-improved antibodies. For the top 14 candidates in the list, perresidue contributions on the antigen side and on the antibody side werefurther analyzed to examine the impact of the proposed modifications.The 10 mutants selected for in vitro site-directed mutagenesis wereTyr172Arg, Arg101Glu, Leu99Asn, Leu99His, Arg101 Asp, Leu217Gln,Leu99Thr, Leu217Asn, Arg101Gln and Asn35Gly. The results can be seen inExample 21.

Example 21 Site-Directed Mutagenesis Confirming the Model for 13.1.2

This example demonstrates one method by which the above models, whichsuggest residues that are important in binding, can be tested. TheExample also results in several antibody variants. Antibody variants of13.1.2 were generated by single residue mutations introduced into theheavy and the light chains of the 13.1.2 mAb. The variants were analyzedto determine the contribution that the various side chains had inantigen binding. A list of the mutations introduced by site directedmutagenesis are summarized in Table 21.1.

TABLE 21.1 Chain Mutation  1 Light chain (CDR3) Arg101Asp  2 Light chain(CDR3) Arg101Gln  3 Light chain (CDR3) Arg101Glu  4 Light chain (CDR1)Asn35Gly  5 Heavy chain (CDR3) Leu217Asn  6 Heavy chain (CDR3) Leu217Gln 7 Light chain (CDR3) Leu99Asn  8 Light chain (CDR3) Leu99His  9 Lightchain (CDR3) leu99Thr 10 heavy chain (CDR2) Tyr172Arg

Each of the 10 mutations in Table 21.1 was introduced into the heavy orlight chain of the 13.1.2 mAb. Each mutated chain was then transfectedwith the complementary wild-type chain in 293 cells. Supernatants werethen tested for expression and secretion of human IgG antibodies, andfor binding to EGFrVIII antigen. The results, as determined by an ELISA,are summarized in Table 21.2.

TABLE 21.2 Mutation Binding Energy Expression Binding  1 Arg101Asp−81.861 Yes No  2 Arg101Gln −79.596 Yes No  3 Arg101Glu −86.817 Yes No 4 Asn35Gly −79.207 Yes Yes  5 Leu217Asn −79.758 Yes Yes  6 Leu217Gln−80.058 Yes Yes  7 Leu99Asn −83.231 Yes Yes  8 Leu99His −82.639 Yes Yes 9 Leu99Thr −80.035 Yes Yes 10 Tyr172Arg −101.706 Yes Yes 11 WT −75.205Yes Yes

Example 22 Preparation of Egfrviii/Pflag Variant Construct

This example demonstrates how a variant to EGFRvIII can be made. A 1092bp fragment encoding the extracellular domain of EGFRvIII was generatedwith primer pairs 9712 and 9713 (Qiagen, Valencia, Calif.):

Primer # 9712: (SEQ ID NO 128) 5′-ataaaagcttctggaggaaaagaaaggtaatta-3′(sense) Primer # 9713: (SEQ ID NO 129)5′-TTATTGGTACCTCAGGCGATGGACGGGATCTTA-3′ (antisense)

from plasmid template EGFRvIII-rbIgG/pCEP4 (as described above)amplified using Pfu DNA polymerase enzyme (Stratagene, La Jolle,Calif.). Primer #9712 introduced a HindIII site and primer #9713introduced a KpnI site. The PCR product was column purified (Qiagencolumn purification kit, Valencia, Calif.) digested with HindIII andKpnI (NEB, New England Biolabs, Beverly, Mass.) and gel purified (Qiagengel purification kit, Valencia, Calif.). Fragments were ligated with T4DNA Ligase (NEB, New England Biolabs, Beverly, Mass.) into pFLAG-CMV-1(Sigma, St. Louis, Mo.) linearized with HindIII and KpnI (NEB, NewEngland Biolabs, Beverly, Mass.). The resulting vector was designatedEGFRvIII/pFLAG-CMV-1 #1.

Example 23 Preparation of EGFRvIII/pFLAG Recombinant Protein

This example demonstrates how a variant EGFRvIII protein can be made.First, 500 μg of EGFRvIII/pFLAG-CMV-1#1 plasmid DNA was resuspended in25 ml of Opti-MEMI (Invitrogen, Burlington, ON) and combined with 500 μlof 293fectin (Invitrogen, Burlington, ON) resuspended in 25 ml ofOpti-MEMI. The mixture was incubated for 20 min at room temperature thenmixed with 293T cells (1×10⁹) prepared in 1 L 293 FreeStyle media(Invitrogen, Burlington, ON), supplemented with 2% FBS and 50 μg/ml G418(Invitrogen, Burlington, ON). Cells are grown for 7 days at 37° C. in 8%CO₂ with shaking at 125 rpm.

EGFRvIII-FLAG fusion protein purification was carried out with Anti-FLAGM2 Affinity Chromatography kit (Sigma, St. Louis, Mo.) according to themanufacture's protocol.

Monomeric fusion protein was produced as follows. First, purifiedprotein (1508 μg), was reduced with DTT in a final concentration of 10mM for 30 minutes at 55° C. Then IAA (iodoacetic acid) (Sigma, St.Louis, Mo.) was added to 22 mM and incubated 15 minutes at roomtemperature in the dark then dialyzed against PBS at 4° C. in 7 k MWCOdialysis cassettes (Pierce, Rockford, Ill.).

Examples 24-30 Binding Studies Of Antibody Variants

The following examples involve Biacore experiments (surface plasmonresonance) and KinExA experiments. These examples demonstrate how onecan test the various antibodies and variants thereof produced by theabove examples to determine if they have the desired bindingcharacteristics. All of the variants examined were variants in the13.1.2 background.

Instrumentation

All surface plasmon resonance experiments were performed using Biacore2000 optical biosensors (Biacore, Inc., Piscataway, N.J.). All KineticExclusion Assays were performed using a KinExA 3000 instrument (SapidyneInstruments, Inc., Boise, Id.).

Reagents

Pep-3, NH₂-LEEKKGNYVVTDHG-OH (MW=1590 Da) (SEQ ID NO: 130), was customsynthesized and purchased from Anatech, Inc. (San Jose, Calif.). AllmAbs were prepared in-house. The antigen EGFRvIIIpflag (iodoacetic acidreacted in order to block aggregation through free sulfhdryl groups), MW39,907, was prepared in-house. Bovine serum albumin (BSA) fraction V (#BP1605-100) was purchased from Fisher Scientific (Pittsburgh, Pa.). Allother general reagents were purchased from Sigma-Aldrich, Inc (St.Louis, Mo.).

All antigen and mAb samples for Biacore and KinExA analysis wereprepared in vacuum-degassed HBS-P buffer (0.01 M HEPES, 0.15 M NaCl,0.005% surfactant P-20, Biacore Inc., Uppsala, Sweden) containing 100μg/mL BSA. Biacore amine-coupling reagents,1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC),N-hydroxysuccinimide (NHS), and ethanolamine were purchased fromBiacore, Inc. Biacore surface regeneration was with a 12 second pulse of26 mM NaOH for the pep-3/mAb 131 experiment. All other mAbs dissociatedto baseline within 20 minutes. Research grade CM5 biosensor chips werepurchased from Biacore, Inc.

The KinExA detection antibody was Cy5-labeled goat anti-human IgG, Fcγspecific (Jackson ImmunoResearch Laboratories, Inc., West Grove, Pa.,#109-175-008) and was diluted 1000-fold in HEPES buffer (0.01 M HEPES,0.15 M NaCl, pH 7.2) from a 0.5 mg/mL stock (1×PBS, pH 7.4). The solidphase particles used for the KinExA experiments were NHS-activatedSepharose 4 Fast Flow beads (Pharmacia Biotech AB, Uppsala, Sweden,#17-0906-01). Prior to reacting the sepharose beads with antigen, a beadstock aliquot of 1.5 mL in a microcentrifuge tube was spun down andwashed at least six times with cold deionized H₂O. After rinsing thebeads once with sodium carbonate buffer (0.05 M, pH 9.3), antigen (˜40μg) in sodium carbonate buffer was added to the sepharose beads. Thesepharose/antigen tube was rocked overnight at 4° C. After rocking, thesepharose was spun and rinsed twice with 1 M Tris buffer, pH 8.3. Theantigen-coated beads were then rocked for 1 hour at room temperature in1 M Tris buffer with 2% BSA.

Biacore Measurements

Standard EDC/NHS and carbohydrate coupling was used to covalentlyimmobilize mAbs to a CM5 sensor chip. To minimize mass transport andcrowding mAbs were immobilized at levels that gave a maximum antigenbinding response (R_(max)) of no more than 50-100 RU. A reference flowcell on each chip was activated and blocked with no mAb immobilizationto serve as a control.

All Biacore kinetic experiments were conducted at 23° C. For eachexperiment, a series of six to eight antigen concentrations (startingwith 1.01 μM pep-3) was prepared using 2-fold dilutions. Antigen sampleswere randomly injected over the biosensor surface in triplicate at 100μL/min. Several buffer blanks were injected intermittently over thecourse of an experiment for double referencing. Each pep-3 concentrationand blank were injected for 90 seconds. Dissociation was followed for 13to 180 minutes. Dissociation data for pep-3 binding to mAb 131 wereacquired by alternating three additional injections of 251 nM pep-3 withthree additional blank injections and following the dissociation phasefor 3-4 hours.

All Biacore sensorgrams were processed using Scrubber software (Version1.1f, BioLogic Software, Australia). Sensorgrams were first zeroed onthe y-axis and then x-aligned at the beginning of the injection. Bulkrefractive index changes were removed by subtracting the reference flowcell responses. The average response of all blank injections wassubtracted from all analyte and blank sensorgrams to remove systematicartifacts between the experimental and reference flow cells. CLAMPbiosensor data analysis software (Version 3.40, BioLogic Software,Australia) was used to determine k_(a) and k_(d) from the processed datasets. Data from all flow cells were globally fit to a 1:1 bimolecularbinding model that included a mass transport term. For several of themAbs the injections corresponding to the first or second concentrationof the pep-3 series were excluded in the nonlinear kinetic fit where itwas obvious that the sensorgrams were not described well by a 1:1interaction model. The K_(D) was calculated from the quotientk_(d)/k_(a).

KinExA Equilibrium Measurements

All KinExA experiments were conducted at room temperature (˜23° C.). Forall equilibrium experiments, antigen was serially diluted into solutionshaving a constant mAb binding site concentration. For the first 10titration points the dilutions were 2-fold and the 11^(th) and 12^(th)serial dilutions were 10-fold. The sample flow rate for all experimentswas 0.25 mL/min and the labeling antibody flow rate was 0.5 mL/min.Antigen/antibody samples were then allowed to reach equilibrium, whichtook ˜48-72 hr to reach. For the pep-3/mAb 131 KinExA experiment thestarting concentration of pep-3 in the K_(D)-controlled titration was352 nM and the constant [mAb binding site]=219 pM; for themAb-controlled titration the starting [pep-3]=251 nM and the [mAbbinding site]=11 nM. During the K_(D)-controlled experiment withpep-3/mAb 131, 1.25 mL of each sample was drawn through the flow cell. Asample volume of 250 μL was analyzed for the antibody-controlledexperiment. Two or three replicates of each sample were measured for allequilibrium experiments. The equilibrium titration data were fit in adual curve analysis to a 1:1 binding model using KinExA software(Version 2.4, Sapidyne Instruments).

The EGFRvIIIpflag/mAb 131 complex was studied with KinExA underK_(D)-controlled conditions only. The starting [EGFRvIIIpflag] was 198nM and the [mAb binding site] was 150 pM. A sample volume of 1 mL wasdrawn through the flow cell. Duplicate measurements were collected forall samples. The equilibrium titration data were fit in a dual curveanalysis to a 1:1 binding model using KinExA software (Version 2.4,Sapidyne Instruments). See Example 28 below for results and predictedequilibrium constant.

For the KinExA titrations of the EGFRvIIIpflag/mAb 13.1.2 complex thestarting concentration of EGFRvIII was 5.26 μM (mAb-controlled), 230.1nM (K_(D)-controlled) and [mAb binding site]=9.59 nM (mAb-controlled),498 pM (K_(D)-controlled). During the K_(D)-controlled experiment, 1.30mL of each sample was drawn through the flow cell. A sample volume of250 μL was analyzed for the antibody-controlled experiment. Two or threereplicates of each sample were measured for all equilibrium experiments.The equilibrium titration data were fit in a dual curve analysis to a1:1 binding model using KinExA software (Version 2.4, SapidyneInstruments).

Example 24 In Vitro Determination of Binding Constants for Antibodies

The binding kinetics of the wild type mAb 131 was observed by using aSurface Plasmon Resonance (SPR) instrument from Biacore. The K_(D) wasvery low, 380 pM, owing to the very slow k_(d) and a rapid k_(a).Estimates for the other kinetic parameters, derived from curve fitting,were k_(a)=2.246*10⁶ and k_(d)=8.502*10⁻⁴.

In one embodiment, improved or variant antibodies with improved kineticsare taught. By improved kinetics, it is meant that one of the kineticelements of antibody binding to an epitope is superior to the sameelement in previously known antibodies for the same epitope. Forexample, an antibody that binds to pep-3 with a K_(D) of greater (inbinding ability) than 1.3*10 M would be an improved antibody. As such,antibodies with a K_(D) of less than 500 nM, 500-300 nM, 300-100 nM,100-1 nM, 1.3 nM, 1.3 nM to 1000 pM, 1000 pM to 900 pM, 900-500 pM,500-400 pM, 400-300 pM, 300-100 pM, 100-50 pM, 50-1 pM, or smaller K_(D)are contemplated.

Example 25 In Vitro Determination of Binding Constants for Antibodies

Similar to Example 24, the binding kinetics of mAb13.1.2 to Pep-3(EGFRvIII epitope) were examined. The estimated K_(D) was 67 nM, butvaried slightly between experiments. Estimates, for the other kineticparameters, derived from curve fitting, were k_(a)=2.835*10⁵ andk_(d)=0.01922.

Example 26 In Vitro Determination of Binding Constants for Antibodies

Similar to Example 24, the binding kinetics of mAb 095 to Pep-3(EGFRvIII epitope) were examined. The estimated K_(D) was 66 nM.Estimates, for the kinetic parameters, derived from curve fitting, werek_(a)=1.491*10⁵ and k_(d)=9.927*10⁻³.

Example 27 In Vitro Determination of Binding Constants for Antibodies

Similar to Example 24, the binding kinetics of mAb 139 to Pep-3(EGFRvIII epitope) were examined. The estimated K_(D) was 290 nM.Estimates, for the kinetic parameters, derived from curve fitting, werek_(a)=10328 and k_(d)=2.981*10⁻³.

Example 28 In Vitro Determination of Binding Constants for Antibodies

In order to more fully analyze the binding characterisitics of theantibodies, KinExA experiments were performed to determine the bindingcharacterisitics of the mAb 131. The K_(D) determined from a dual curveanalysis was 1.74*10⁻¹°. In a KinExA experiment, the K_(D) forEGFRvIIIpflag to mAb 131 was 6.266*10⁻¹¹.

Example 29 In Vitro Determination of Binding Constants for VariantAntibodies

In order to more fully analyze the binding characterisitics of the13.1.2 antibodies, a KinExA experiment was performed to determine thebinding characterisitics of the mAb 13.1.2. The K_(D) determined from adual curve analysis was 7.538*10⁻¹°. Additionally, the antigen in thisexample was the EGFRvIIIpflag variant and was reacted with iodoaceticacid (IAA).

Example 30 Comparison of Biacore Results and Kinexa Results

The results of the previous Examples and the KinExA tests are presentedin Table 30.1 below. Numbers in parentheses in Table 30.1 are 95%confidence intervals. “ND,” means not determined and “*” denotes bindingto EGFRvIIIpflag (iodoacetic acid reacted), instead of pep-3.

As is evidenced by the rate constants, mAb 131 appears to have thegreatest association constant and the lowest dissociation constant, thusgiving mAb 131 the lowest K_(D).

TABLE 30.1 MAb K_(a) (M⁻¹s⁻¹) K_(d) (s⁻¹) K_(D) (nM) KinExA K_(D) (nM)131 2.25 × 10⁶ 8.50 × 10⁻⁴ 0.380 0.174 (0.0627 on EGFRvIIIpflag) 13.1.22.10 0.016 75 0.75 (on (0.58) × 10⁵  (0.003) (14) EGFRvIllpflag (IAAreacted)) 095 1.49 × 10⁵ 9.90 × 10⁻³ 66 ND 139 1.03 × 10⁴ 2.98 × 10⁻³290 ND

Example 31 In Vitro Determination of Binding Constants for L99T-5.3Variant Antibodies

The binding kinetics of mAb L99T-5.3 to Pep-3 (EGFRvIII epitope) wereexamined. The first step was to immobilize 5,600 resonance units (RU) to8,000 RU of mAb L99T-5.3 to two flow cells (Fc) of a CM5 sensor chip and5,600 resonance units (RU) to 8,000 RU of mAb 13.1.2 to one Fc usingstandard EDC/NHS coupling chemistry. This surface density yielded abinding signal with pep-3 of less than 100 RU. Two CM5 sensor chips wereused in total to immobilize both mAbs. With the previously collecteddata, this produced a total of 5 independent experiments for bothantibodies that allows the 95% confidence intervals to be calculated.Biacore 2000 optical biosensors were used for all studies.

Next, pep-3 was flowed across the mAb immobilized biosensor surfaces.The starting concentration of pep-3 was 1.25 μM, which was followed witheight two-fold serial dilutions in randomized triplicate injections.Blank injections were run every sixth sample throughout the injectionseries for double referencing purposes.

Finally, the biosensor data was processed with Scrubber and the data wasfit to curves utilizing Clamp with a 1:1 interaction model with a termincluded for mass transport. The high concentration injections, 1.25 μM,were excluded from the kinetic fits because it was apparent that thedata was not consistent with a 1:1 interaction model. Most likely, thisdeviation is caused by non-specific interactions occurring at highconcentrations of pep-3. All the kinetic data fit a 1:1 interactionmodel satisfactorily.

The estimated K_(D) varied from 54-70 nM. Estimates, for the otherkinetic parameters, which also varied slightly between runs, werek_(a)=2.238*10⁵ and k_(d)=0.01217.

Examples 32-38

Examples 32-38 further examined the binding kinetics of the variant mAbsthrough the use of a Biacore device. The first step in these examplesinvolved the immobilization of 5,600 resonance units (RU) to 8,000 RU ofeach mAb tested to one flow cell (Fc) of a CM5 sensor chip usingstandard EDC/NHS coupling chemistry. This surface density yielded abinding signal with pep-3 of less than 100 RU. Three CM5 sensor chipswere used in total to immobilize all mutant mAbs with a unique mAbimmobilized to each flow cell. MAb 13.1.2 was included on one flow cellfor two out of the three CM5 sensor chips. Biacore 2000 opticalbiosensors were used for all studies.

Next, pep-3 was run across the mAb immobilized biosensor surfaces. Thestarting concentration of pep-3 was 4.98 μM, followed by eight to eleventwo-fold serial dilutions in randomized duplicate or triplicateinjections. Blank injections were run every sixth sample throughout theinjection series for double referencing purposes.

Finally, the biosensor data was processed with Scrubber and fittedutilizing Clamp with a 1:1 interaction model with a term included formass transport. Some high concentration injections (4.98-1.25 μM),depending upon the mAb and its affinity, were excluded from the kineticfits when it was apparent that the data was not consistent with a 1:1interaction model. Most likely, this deviation is caused by non-specificinteractions occurring at high concentrations of pep-3. All the kineticdata fit a 1:1 interaction model.

Example 32 In Vitro Determination of Binding Constants for L2170-10.1Variant Antibodies

The binding kinetics of mAb L217Q-10.1 to Pep-3 (EGFRvIII epitope) wereexamined. The estimated K_(D) was 92 nM. Estimates, for the otherkinetic parameters, derived from curve fitting, were k_(a)=2.04*10⁵ andk_(d)=0.01885.

Example 33 In Vitro Determination of Binding Constants for L217N-2.1Variant Antibodies

Similar to Example 32, the binding kinetics of mAb L217N-2.1 to Pep-3(EGFRvIII epitope) were examined. The estimated K_(D) was 185 nM.Estimates, for the other kinetic parameters, derived from curve fitting,were k_(a)=2.198*10⁵ and k_(d)=0.04069.

Example 34 In Vitro Determination of Binding Constants for N35G-3.1Variant Antibodies

Similar to Example 32, the binding kinetics of mAb N35G-3.1 to Pep-3(EGFRvIII epitope) were examined. The estimated K_(D) was 204 nM.Estimates, for the other kinetic parameters, derived from curve fitting,were k_(a)=1.497*10⁵ and k_(d)=0.03057.

Example 35 In Vitro Determination of Binding Constants for VariantAntibodies

Similar to Example 32, the binding kinetics of mAb L99H-9.2 to Pep-3(EGFRvIII epitope) were examined. The estimated K_(D) was 395 nM.Estimates, for the other kinetic parameters, derived from curve fitting,were k_(a)=83390 and k_(d)=0.03293.

Example 36 In Vitro Determination of Binding Constants for VariantAntibodies

Similar to Example 32, the binding kinetics of mAb Y172R-1.2 to Pep-3(EGFRvIII epitope) were examined. The estimated K_(D) was 927 nM.Estimates, for the other kinetic parameters, derived from curve fitting,were k_(a)=82237 and k_(d)=0.07622.

Example 37 In Vitro Determination of Binding Constants for VariantAntibodies

Similar to Example 32, the binding kinetics of mAb L99N-4.1 to Pep-3(EGFRvIII epitope) were examined. The estimated K_(D) was 1.4 μM. MAbL99N-4.1 was fit using a steady-state (equilibrium) binding model inorder to determine the K_(D) because the kinetics were too fast to befitted.

Example 38 Comparison of 13.1.2 with Designed Variants

As can be seen in Table 38.1 a mAb with improved binding characteristicswas developed. The 95% confidence intervals are shown in parentheses.L99T-5.3 exhibited an enhanced k_(a), a decreased k_(d), and thus aslower K_(D) overall. While statistically there appears to be little ifany significant difference in the equilibrium dissociation constants andkinetic rate constants of Pep-3 binding to mAbs 13.1.2 and L99T-5.3 (atthe 95% confidence interval), there still seems to be an intuitive biasfor a marginal increase in affinity for Pep-3 binding to L99T-5.3.Moreover, when the same biosensor chip was used, L99T-5.3 seemed toalways have a higher affinity than 13.1.2.

TABLE 38.1 MAb k_(a) (M⁻¹s⁻¹) k_(d) (s⁻¹) K_(D) (nM) 13.1.2 2.10 (0.58)× 10⁵ 0.016 (0.003) 75 (14) L99T-5.3 2.16 (0.12) × 10⁵ 0.013 (0.001) 60(10) L217Q-10.1 2.04 × 10⁵ 0.019  92 L217N-2.1 2.20 × 10⁵ 0.040 185N35G-3.1 1.50 × 10⁵ 0.030 204 L99H-9.2 8.34 × 10⁴ 0.033 395 Y172R-1.28.22 × 10⁴ 0.076 927 L99N-4.1 ND ND 1,400* 

Additional Docking Models and Methods of Selecting Models and PredictingBinding Affinity

In other embodiments, the examples described above can be performed withvarious length peptides rather than just peptides that are 6 amino acidsin length, as long as the key binding residues are included in thepeptide. For example, instead of the six amino acid peptide, EEKKGN (SEQID NO: 127), a seven amino acid peptide, EEKKGNY (SEQ ID NO: 131) can beused. Any size peptide for the epitope can be used. In otherembodiments, the peptide is selected from the following peptides:LEEKKGNYVVTDHC (SEQ ID NO: 56), LEEKKGNYVVTD (SEQ ID NO: 59),LEEKKGNYVVT (SEQ ID NO:132), and EEKKGNYVVT (SEQ ID NO:57). Any sizedpeptide between the short fragments disclosed herein, to the full lengthpeptide, or variants thereof, can be used.

As appreciated by one of skill in the art, the presence of additionalamino acids can alter the manner in which the peptide binds to theantibody. Not only does the presence of the additional amino acid allowfor alternative and additional bonds to be formed between the peptideand the antibody, but the additional amino acid can change the structureof the peptide and the structure of the antibody upon binding of thepeptide with the antibody. Thus, in one embodiment, various lengths ofthe epitope peptide, e.g. EEKKGN (SEQ ID NO: 127) and EEKKGNY (SEQ IDNO: 131), can be examined for binding properties and bindingoptimization. Not only will the longer fragments of the peptide providean accurate depiction of the peptide-antibody interaction for longersegments of the peptide, but an examination of the changes in bindingstrength and the residues involved in binding will allow additionalinformation concerning longer peptides to be extrapolated from the data.

In addition, and perhaps complementary to the testing of longer peptidefragments, additional filtering steps can be performed on the variousdocking models in order to select a refined docking model. An additionalfiltering step can allow one to filter through numerous docking modelsto find those that are consistent with available experimental data.

In one embodiment, the filter is based on fine-resolution epitopemapping data, e.g., the experimentally characterized individual residuebinding profile, which could be correlated with the computed bindingenergy profile for each amino acid in the peptide. The binding energyprofile of a seven amino acid peptide, for example, can be used toselect docking models that contain similar binding energy profiles. Abinding energy profile is an assignment of the binding energy of eachamino acid in a peptide to the particular amino acid to create a profileof the peptide in terms of each amino acid's binding energy in thatmodel. For example, in one docking model, given a peptide comprisingamino acids A and B, where A has a binding energy of −5 and B has abinding energy of −20, one would have a profile of A1 (at −5) and B2 (at−20). This profile could be used as a filter to select other dockingmodels. For example, the use of this binding energy profile as a filteror “template” would result in other docking models being selected if thepeptide in the candidate model had a relatively low value attributed toposition A, and a relatively high (larger negative, higher absolutevalue) value attributed to position B. In an alternative embodiment, thetemplate requires additional limitations; for example, that the value atposition B is four fold higher than the value at position A.

One can compare the binding energy profile template with the profiles ofthe peptide in the other docking models in a variety of ways. If thebinding energy profile template is similar to the desired binding energyprofile, then the filter can be used to pick out favorable dockingmodels for further examination. If the binding energy profile templateis dissimilar to the desired binding energy profile, then the filter canbe used to eliminate unfavorable docking models. In one embodiment, thefiltering process includes a template with both favorable andunfavorable binding energies and the filter is used to both select andexclude docking models. As appreciated by one of skill in the art, thereare many possible different binding energy profiles, and thus manydifferent binding energy profile templates that can be used dependingupon the situation.

In one embodiment, one can define a binding energy profile template as atemplate that has a series of relatively high binding energies atparticular positions in the peptide. In a preferred embodiment, thebinding energy profile template, and the binding energy profile selectedby the template, will have relatively high binding energy at position 2,4, or 6 of the peptide, EEKKGNY (SEQ ID NO: 131). In another embodiment,the binding energy profile template will have a relatively high bindingenergy at positions 2, 4, and 6 of the peptide EEKKGNY (SEQ ID NO: 131).In another embodiment, the binding energy profile template will have arelatively low binding energy attributed to position 3 of the peptideEEKKGNY (SEQ ID NO: 131). In the above discussion, the positions areassigned as follows: E1, E2, K3, K4 G5, N6, Y7.

In one embodiment, the filtering process first involves a comparison ofthe binding energies at K3 and K4. Docking models that result in arelatively higher binding energy for K4 compared to K3 are selected,while docking models that result in a lower binding energy for K4compared to K3 are filtered out. Thus, by “relatively high,” it is meantthat the binding energy for K4 is greater (more negative value, largerabsolute value) than K3. Next, the docking models are again filteredthrough the binding energy profile template, this time, those bindingmodels with relatively higher energies at positions 2, 4, and 6 areselected for, while the other models can be removed. Thus, by“relatively high,” it is meant that the binding energy at positions 2,4, and 6 are higher (more negative value, larger absolute value) thanthe lowest binding energy in the peptide. Thus, in this embodiment, thebinding energy profile template could be summarized as follows: E1 canbe any value, E2 should be greater than the lowest value, K3 should beless than K4, K4 should be greater than the lowest value, G5 can be anyvalue, N6 should be greater than the lowest value, Y7 can be any value.Thus, E1, G5, and Y7 could be any value, as long as at least one (or K3)is lower than at least one of E2, K4, and N6. In another embodiment,“relatively high” can be set to a standard value as determined throughmodeling or experimentation. In one embodiment, that the docking modelspass the first filter is more important than the docking model pass thesecond filtering step. As appreciated by one of skill in the art, oneneed not perform these two steps sequentially and they can be performedsimultaneously.

Additionally, these profile templates for filtering through results willvary depending upon the peptide, the antibody, and the bindingconditions. One of skill in the art, given the present disclosure,especially with reference to Example 14, could determine the appropriatebinding energy profile template. For example, as shown in Table 14.1,there are several possible important residues for peptide binding bothin the 131 and in the 13.1.2 antibody. In the 131 mAb, positions E2, K4,N6, and Y7 are important for the particular peptide tested. In the13.1.2 mAb, positions E1, E2, K4, G5, and N6 are important for theparticular peptide tested. Those residues that are important can beresidues involved in the creation of a binding energy profile template.As clear from the discussion below, the binding energy profile templatein Example 39 appears to be different from that suggested by an analysisof Example 14. Example 39 is a less stringent version of the templatethat allows more models to pass through the screening step. If onewanted to reduce the number of models that made it through the screeningstep, one could further add requirements concerning E1 and G5.

The following example demonstrates both the use of a longer peptide, howit can alter the results demonstrated above, what such changes can mean,as well as demonstrating the use of one of the above filters forselecting particular docking models.

Example 39 Epitope-Antibody Docking Model for a Seven Amino Acid Peptide

This example demonstrates the generation of a set of docking models fora seven-residue peptide complexed to the CDR region of 13.1.2 structuremodel. Additionally, this example demonstrates methods for selecting onedocking model over another docking model.

First, a structural model for the seven-residue peptide EEKKGNY (SEQ IDNO: 131) was built in an extended conformation and energy minimized withDiscover_3 module in InsightII modeling package. Next, the peptidestructure was manually placed into the combining site to form an initialassembly. A Monte Carlo search in the translational and rotationalspaces was then automatically performed with relaxed energy constraintsin the Docking module in InsightII. During the docking process, theresidues within 5 Angstroms of the binding groove were allowed to movewhile other antibody residues were fixed. The peptide was constrained towithin 5 Angstroms of the starting position. The plausibleconfigurations found by the Monte Carlo search were followed bysimulated annealing and energy minimization to reach the final complexstructure models. A total of 63 docking models were obtained.

For each docking model, the interaction energy between the antibody andthe individual residue in the peptide was calculated with Discover_3.The profile of individual residue contribution in epitope-antibodybinding was inspected to select the docking models that are consistentwith the fine-resolution epitope mapping data, i.e., “the binding energyprofile template.” 19 out of 63 docking models passed this check. Atypical individual residue binding energy profile is shown in Table39.1. Consistent with the epitope mapping data, in Example 14, thebinding energy for K4 is prominent, and those for N6 and E2 are large.This binding energy profile template placed particular emphasis on thefact that K4 is greater than K3. This binding energy profile also placedan emphasis on the requirement that E2, K4, and N6 are relatively large.In other words, the binding energies of E2, K4, and N6 were not thelowest (least negative or smallest absolute value) binding energies inthe peptide.

TABLE 39.1 Binding Energy Profile For Individual Residue In TheSeven-Residue Peptide To Antibody 13.1.2 Is Consistent With EpitopeMapping Data In Example 14. E1 E2 K3 K4 G5 N6 Y7 Total −10.97 −19.34−13.46 −24.26 −10.1 −18.19 −15.15 −111.45

For the 19 models that passed the filter based on the binding energyprofile, epitope-antibody binding energetics simulations were performedon each of the seven mutants with affinity data (Tyr172Arg, Example 36;Leu217Asn, Example 33; Leu217Gln, Example 32; Asn35Gly, Example 34;Leu99Asn, Example 37; Leu99His, Example 35; and Leu99Thr, Example 31).Since the extent of electrostatic interaction in this complex had to beapproximated, a number of different dielectric constants were used in aseries of calculations. The mutation was done with residue replacementfollowed by 30-100 steps of energy minimization to account for any localconformational changes that are induced by the side chain change. Foreach docking model, the interaction energy between the seven-residuepeptide and the whole antibody was calculated for each mutant for theselected parameters. For each set of 8 binding energies (7 mutants plusthe wild type), a linear fitting procedure was done on each set of thebinding data, in comparison with the logarithm of Kd. A correlationcoefficient was calculated for each linear fitting. The best correlationwas obtained for one model, the model with the data described in Table39.1, with a dielectric constant 1*r and 50 steps of energyminimization. The epitope-antibody binding energies for this model areshown in Table 39.2. The correlation coefficient was 0.80 with all thedata. As the K_(D) for Leu99Asn was not measured with high degree ofaccuracy, see Example 37 above, a separate linear fitting was performedexcluding the data for Leu99Asn. An excellent correlation coefficient of0.91 was obtained, as shown in FIG. 14. The refined docking model isthus well represented by the above selected model. The model withspace-filling peptide is shown in FIG. 15, and the hydrogen bonds areshown in FIG. 16. L3 150 is the lower section and H3 160 is the uppersection on FIG. 16. H2 140 is to the right of the peptide binding area.The peptide itself is placed into the binding site with E1 beingpositioned at the top of the page in a light shade, down through K3, K4,G5, N6, and Y7, progressively getting darker. The antibody residuesinvolved in hydrogen bonding are shown in FIG. 16. The model producedfrom this example demonstrates that there are seven hydrogen bonds: K4 .. . Q95, K4 . . . Q95, N6 . . . Q98, G5 . . . H31, Y7 . . . H31, and Y7. . . W165.

TABLE 39.2 Simulation Of Epitope-Antibody Binding Energetics, InComparison With Logarithm Of Kd. mutant coulumbic vdw total Ln(Kd)172Arg −19.103 −27.962 −47.065 −13.891 217Asn −19.003 −28.715 −47.718−15.503 217Gln −18.977 −28.73 −47.707 −16.201 35Gly −19.095 −28.431−47.526 −15.405 99Asn −18.719 −28.778 −47.497 (−13.479) 99His −18.837−28.719 −47.556 −14.744 99Thr −19.155 −28.704 −47.859 −16.475 WT −18.981−28.728 −47.708 −16.269

As can be seen from the model selected in Example 39, which isrepresented in FIG. 15, the docking model revealed some unexpectedresults. One interesting result is that while residues E2, K4, and N6are important residues in the binding of the peptide as a whole, not allof these amino acids are modeled as involved in forming H-bonds with theantibody. It appears that K4 is involved in the formation of twoH-bonds, both with Q95, which is consistent with K4's importance in thebinding energy profile and profile template. It also appears that N6 ismodeled to bond to Q98; however, in this particular model, E2 does notappear to form H-bonds in the model. One interesting trend that isconsistent is that each of the key residues from the binding energyprofile template (e.g., E2, K4, and N6) are mostly buried and thus inclose contact with the antibody binding groove. Thus, this docking modelselection can account for the fact that these key residues are importantbecause of their close interaction with the antibody. Additionally, itis possible that E1 is involved in a hydrogen bond with W214.

Example 39 also demonstrates that the above described method results ina strong correlation between binding energy and K_(D), suggesting thatmodels created by this method will also allow optimization or at least aprediction of the K_(D) of the antibody-peptide complex.

As can be seen from a comparison of Example 39 and Example 19, there aresome residues that are important between the two models, some residuesthat appear only in the seven amino acid docking model, as well as someresidues that do not appear to be as important in the seven amino aciddocking model. For example, the seven peptide epitope appears to createH bonds between K4 . . . Q95, K4 . . . Q95, N6 . . . Q98, G5 . . . H31,Y7 . . . H31, and Y7 . . . W165. On the other hand, the six peptideepitope appears to create H bonds between E2 . . . Y172, K3 . . . H31,K4 . . . H31, N6 . . . D33, N6 . . . Y37, and N6 . . . K55. As can beseen from the above data, both the six and the seven amino acid peptidemodels emphasize the importance of H 31, as both models involve H31forming two hydrogen bonds with the peptide. While there are otherpossible trends between the two data sets, it also appears that many ofthe binding interactions have changed from the six amino acid model tothe seven amino acid model. However, these examples demonstrate thatvariations due to epitope size can be detected with these models andthus the scaling up from shorter to longer epitope peptides should notbe problematic in light of the present disclosure. The presence of aminoacids that consistently demonstrate their importance in various bindingmodels allows one to bias the importance of the various interactionsaccordingly so that shorter peptide models can be more representative oflonger peptide interactions.

As appreciated by one of skill in the art, any of the above discussionor examples concerning the six amino acid peptide, EEKKGN (SEQ ID NO:127), can also be applied towards the seven amino acid peptide, EEKKGNY(SEQ ID NO: 131), or any longer peptide. For instance, Example 20 can berepeated with the information from Example 39 for rational design foraffinity-improved antibodies by site-directed mutagenesis. Furthermore,Example 21 can be repeated, using the results of Example 39, followingan attempt of rational design for affinity-improved antibodies bysite-directed mutagenesis to test any new antibodies derived fromExample 20.

In one embodiment, the results from Example 39 are used to redefine theinteraction area between the antibody and the peptide. For example, theparatope, for EEKKGNY (SEQ ID NO: 131), can be defined as including theother residues on the antibody that are predicted to interact with thepeptide, for example, residue 95. Alternatively, as in Example 19, theparatope can be defined as all residues within 5 Angstroms of the dockedpeptide.

In Silico Affinity Maturation in Different Proteins

Antibody affinity maturation has been successfully done in vitro in anumber of different studies. Typically, randomized mutant libraries needto be constructed by molecular biology methods and selection/screeningassays need to be developed to enrich the clones with good bindingcapability. Selected variants then need to be purified to determineaffinities. This process requires a series of lengthy and laboriousexperiments. The following example demonstrates that it is possible toaccurately predict affinity maturation through in silico selectionutilizing an antibody-antigen complex structure alone.

Example 40 In Silico Affinity Maturation Through Antibody-AntigenBinding Energetics Simulations

This Example demonstrates that in silico antibody-antigen bindingenergetics simulations can be used for affinity maturation. Inparticular, this example demonstrates that the binding kinetics of aFab-12 (IgG form known as rhuMAb VEGF) to VEGF (vascular endothelialgrowth factor) can be predicted through the above described in silicoprocess.

The crystal structure of the VEGF-Fab complex used was located in thePDB database with the accession number 1BJ1, at a resolution of 2.4angstroms. Published experimental affinity data for a series of mutantsof an anti-VEGF Fab were used to test the concept. The 3-D coordinatesof the VEGF-Fab structure were used for carrying out in silico mutationfor the following mutants: H97Y, S100aT, T28D, 28D31H, 28D31H97Y100aT,N31H, Y53W, 71I73K, 71V73V. The affinity data were obtained from thepaper by Chen, Y et al., (J Mol Biol., 293(4):865-81 (1999)). Theenergetics simulations were carried out between the various VEGF-Fabmutants, as described in Example 39. The results are listed in Table40.1. The results from this example demonstrate that a significantcorrelation between the binding energy and affinity ranking was obtainedthrough this process. The linear fitting of the binding energy versuslogarithm of the relative affinity is shown in FIG. 17. The correlationcoefficient of −0.91 indicates that the in silico simulation accuratelycaptures the detailed interaction at the atomic level.

TABLE 40.1 Antibody-Antigen Binding Energy Simulation Compared WithAffinity Kabat Number Sequence Number Relative Affinity Ln(RelativeAffinity) BindingEnergy H97Y 101Y 14 2.639 −59.065 S100aT 105T 1.9 0.642−57.465 T28D 28D 1.4 0.336 −57.647 28D31H 28D31H 3.1 1.131 −57.69928D31H97Y100aT 28D31H101Y105T 20 2.996 −59.518 N31H 31H 3.6 1.281−57.724 Y53W 54W 1.3 0.262 −57.504 71I73K 72I74K 0.9 −0.105 −57.15871V73V 72V74V 0.3 −1.204 −57.314 WT WT 1 0.000 −57.404

As is clear from the Examples above, the simulation can be extrapolatedto identify higher affinity mutants without the use of in vitroexperimentation. Additionally, it is clear that this approach is usefulfor different antibodies and for different peptides. This methodologycan be generally applied to perform affinity maturation in silico, usingonly a high-resolution antibody-antigen complex structure. In oneembodiment, this use of in silico affinity maturation will savetremendous amounts of time and resource.

Example 41 Determination of Canonical Classes of Antibodies

Chothia, et al have described antibody structure in terms of “canonicalclasses” for the hypervariable regions of each immunoglobulin chain (J.Mol. Biol. 1987 Aug. 20; 196 (4):901-17). The atomic structures of theFab and VL fragments of a variety of immunoglobulins were analyzed todetermine the relationship between their amino acid sequences and thethree-dimensional structures of their antigen binding sites, Chothia, etal. found that there were relatively few residues that, through theirpacking, hydrogen bonding or the ability to assume unusual phi, psi oromega conformations, were primarily responsible for the main-chainconformations of the hypervariable regions. These residues were found tooccur at sites within the hypervariable regions and in the conservedbeta-sheet framework. By examining sequences of immunoglobulins havingunknown structure, Chothia, et al show that many immunoglobuins havehypervariable regions that are similar in size to one of the knownstructures and additionally contained identical residues at the sitesresponsible for the observed conformation.

Their discovery implied that these hypervariable regions haveconformations close to those in the known structures. For five of thehypervariable regions, the repertoire of conformations appeared to belimited to a relatively small number of discrete structural classes.These commonly occurring main-chain conformations of the hypervariableregions were termed “canonical structures”. Further work by Chothia, etal. (Nature. 1989 Dec. 21-28; 342(6252):877-83) and others (Martin, etal. J Mol Biol. 1996 Nov. 15; 263(5):800-15) confirmed that that thereis a small repertoire of main-chain conformations for at least five ofthe six hypervariable regions of antibodies.

Some of the antibodies described above were analyzed to determine thecanonical class for each of the antibody's complementarity determiningregions (CDRs). As is known, canonical classes have only been assignedfor CDR1 and CDR2 of the antibody heavy chain, along with CDR1, CDR2 andCDR3 of the antibody light chain. The table below (41.1) summarizes theresults of the analysis. The Canonical Class data is in the form of*HCDR1-HCDR2-LCDR1-LCDR2-LCDR3, wherein “HCDR” refers to the heavy chainCDR and “LCDR” refers to the light chain CDR. Thus, for example, acanonical class of 1-3-2-1-5 refers to an antibody that has a HCDR1 thatfalls into canonical class 1, a HCDR2 that falls into canonical class 3,a LCDR1 that falls into canonical class 2, a LCDR2 that falls intocanonical class 1, and a LCDR3 that falls into canonical class 5.

TABLE 41.1 mAb H1-H2-L1-L2-L3 139 1-3-2-1-1 250 1-3-2-1-1 123 1-3-4-1-1131 1-3-4-1-1 13_1_2 1-3-4-1-1 211 1-3-4-1-1 318 1-3-4-1-1 333 1-3-4-1-1342 1-3-4-1-1 95 3-1-4-1-1 150 3-Y-4-1-1 170 3-Y-4-1-1

Each CDR (except for H3) was assigned to a canonical structure if itsatisfies the length requirement and matches the key residues defined inthe canonical class. The amino acids defined for each antibody can befound, for example, in the articles by Chothia, et al. referred toabove.

INCORPORATION BY REFERENCE

All references cited herein, including patents, patent applications,papers, text books, and the like, and the references cited therein, tothe extent that they are not already, are hereby incorporated herein byreference in their entirety.

EQUIVALENTS

The foregoing description and Examples detail certain preferredembodiments of the invention and describes the best mode contemplated bythe inventors. It will be appreciated, however, that no matter howdetailed the foregoing may appear in text, the invention may bepracticed in many ways and the invention should be construed inaccordance with the appended claims and any equivalents thereof.

1. (canceled)
 2. (canceled)
 3. A monoclonal antibody that binds toEGFRvIII comprising: a heavy chain polypeptide comprising the followingcomplementarity determining regions (CDRs): a heavy chain CDR1 that is aCDR1 in SEQ ID NO: 142; a heavy chain CDR2 that is a CDR2 in SEQ ID NO:142; and a heavy chain CDR3 that is a CDR3 in SEQ ID NO: 142; and alight chain polypeptide comprising the following CDRs: a light chainCDR1 that is a CDR1 in SEQ ID NO: 144; a light chain CDR2 that a CDR2 inSEQ ID NO: 144; and a light chain CDR3 that is a CDR3 in SEQ ID NO: 144.4. The monoclonal antibody of claim 3, wherein the heavy chainpolypeptide is part of a murine IgG1 isotype heavy chain.
 5. Themonoclonal antibody of claim 3, wherein the light chain polypeptide ispart of a kappa light chain.
 6. The monoclonal antibody of claim 3,wherein the heavy chain polypeptide comprises all three of the followingamino acid sequences: SEQ ID NO: 121, SEQ ID NO: 123, and SEQ ID NO:125.
 7. The monoclonal antibody of claim 3, wherein the light chainpolypeptide comprises all three of the following amino acid sequences:SEQ ID NO: 101, SEQ ID NO: 116, and SEQ ID NO:
 118. 8. The monoclonalantibody of claim 3, wherein each CDR is defined in accordance with theCDR definition of Kabat.
 9. The monoclonal antibody of claim 3, whereineach CDR is defined in accordance with the CDR definition of Chothia.10. The monoclonal antibody of claim 3, wherein the heavy chainpolypeptide comprises an amino acid sequence that is at least 90 percentidentical to the heavy chain variable region amino acid sequence in SEQID NO:
 142. 11. The monoclonal antibody of claim 3, wherein the lightchain polypeptide comprises an amino acid sequence that is at least 90percent identical to the light chain variable region amino acid sequencein SEQ ID NO:
 144. 12. An monoclonal antibody that binds to EGFRvIIIcomprising: a heavy chain variable region, wherein CDR3 of the heavychain variable region comprises the amino acid sequence of SEQ ID NO:125, wherein CDR2 of the heavy chain variable region comprises the aminoacid sequence of SEQ ID NO: 123, wherein CDR1 of the heavy chainvariable region comprises the amino acid sequence of SEQ ID NO: 121, andwherein the heavy chain variable region comprises an amino acid sequencethat is at least 90 percent identical to the heavy chain variable regionof the amino acid sequence in SEQ ID NO: 142; and a light chain variableregion, wherein CDR3 of the light chain variable region comprises theamino acid sequence of SEQ ID NO: 118, wherein CDR2 of the light chainvariable region comprises the amino acid sequence of SEQ ID NO: 116,wherein CDR1 of the light chain variable region comprises the amino acidsequence of SEQ ID NO: 101, and wherein the light chain variable regioncomprises an amino acid sequence that is at least 90 percent identicalto the heavy chain variable region of the amino acid sequence in SEQ IDNO: 144, wherein the monoclonal antibody comprises a murine IgG1 isotypeheavy chain comprising the heavy chain variable region, wherein themonoclonal antibody comprises a kappa light chain comprising the lightchain variable region, and wherein the monoclonal antibody does notoccur in nature.
 13. A monoclonal antibody that binds to EGFRvIIIcomprising: a heavy chain polypeptide comprising the followingcomplementarity determining regions (CDRs): a heavy chain CDR1 that is aCDR1 in SEQ ID NO: 2; a heavy chain CDR2 that is a CDR2 in SEQ ID NO: 2;a heavy chain CDR3 that is a CDR3 in SEQ ID NO: 2; and a light chainpolypeptide comprising the following CDRs: a light chain CDR1 that is aCDR1 in SEQ ID NO: 19; a light chain CDR2 that a CDR2 in SEQ ID NO: 19;and a light chain CDR3 that is a CDR3 in SEQ ID NO:
 19. 14. Themonoclonal antibody of claim 13, wherein the heavy chain polypeptide ispart of a murine IgG1 isotype heavy chain.
 15. The monoclonal antibodyof claim 13, wherein the light chain polypeptide is part of a kappalight chain.
 16. The monoclonal antibody of claim 13, wherein the heavychain polypeptide comprises all three of the following amino acidsequences: SEQ ID NO: 108, SEQ ID NO: 110, and SEQ ID NO:
 112. 17. Themonoclonal antibody of claim 13, wherein the light chain polypeptidecomprises all three of the following amino acid sequences: SEQ ID NO:101, SEQ ID NO: 103, and SEQ ID NO:
 105. 18. The monoclonal antibody ofclaim 13, wherein the heavy chain polypeptide comprises an amino acidsequence that is at least 90 percent identical to the heavy chainvariable region amino acid sequence in SEQ ID NO:
 2. 19. The monoclonalantibody of claim 13, wherein the light chain polypeptide comprises anamino acid sequence that is at least 90 percent identical to the lightchain variable region amino acid sequence in SEQ ID NO:
 19. 20. Amonoclonal antibody that binds to EGFRvIII comprising: a heavy chainvariable region, wherein CDR3 of the heavy chain variable regioncomprises the amino acid sequence of SEQ ID NO: 112, wherein CDR2 of theheavy chain variable region comprises the amino acid sequence of SEQ IDNO: 110, wherein CDR1 of the heavy chain variable region comprises theamino acid sequence of SEQ ID NO: 108, and wherein the heavy chainvariable region comprises an amino acid sequence that is at least 90percent identical to the heavy chain variable region of the amino acidsequence in SEQ ID NO: 2; and a light chain variable region, whereinCDR3 of the light chain variable region comprises the amino acidsequence of SEQ ID NO: 105, wherein CDR2 of the light chain variableregion comprises the amino acid sequence of SEQ ID NO: 103, wherein CDR1of the light chain variable region comprises the amino acid sequence ofSEQ ID NO: 101, and wherein the light chain variable region comprises anamino acid sequence that is at least 90 percent identical to the lightchain variable region amino acid sequence in SEQ ID NO: 19, wherein themonoclonal antibody comprises a murine IgG1 isotype heavy chaincomprising the heavy chain variable region, wherein the monoclonalantibody comprises a kappa light chain comprising the light chainvariable region, and wherein the monoclonal antibody does not occur innature.
 21. An assay kit for the detection of EGFRvIII in mammaliantissues or cells, the assay kit comprising: a first monoclonal antibodythat binds to EGFRvIII comprising: (a) a heavy chain polypeptidecomprising the following complementarity determining regions (CDRs): aheavy chain CDR1 that is a CDR1 in SEQ ID NO: 142; a heavy chain CDR2that is a CDR2 in SEQ ID NO: 142; a heavy chain CDR3 that is a CDR3 inSEQ ID NO: 142; and a light chain polypeptide comprising the followingCDRs: a light chain CDR1 that is a CDR1 in SEQ ID NO: 144; a light chainCDR2 that a CDR2 in SEQ ID NO: 144; and a light chain CDR3 that is aCDR3 in SEQ ID NO: 144; or (b) a heavy chain polypeptide comprising thefollowing complementarity determining regions (CDRs): a heavy chain CDR1that is a CDR1 in SEQ ID NO: 2; a heavy chain CDR2 that is a CDR2 in SEQID NO: 2; a heavy chain CDR3 that is a CDR3 in SEQ ID NO: 2; and a lightchain polypeptide comprising the following CDRs: a light chain CDR1 thatis a CDR1 in SEQ ID NO: 19; a light chain CDR2 that a CDR2 in SEQ ID NO:19; and a light chain CDR3 that is a CDR3 in SEQ ID NO: 19; and alabeled second antibody that is anti-immunoglobulin.
 22. A method ofusing an assay kit for patient selection, the method comprising:providing an assay kit for the detection of EGFRvIII in mammaliantissues or cells, the assay kit comprising: a first monoclonal antibodythat binds to EGFRvIII comprising: (a) a heavy chain polypeptidecomprising the following complementarity determining regions (CDRs): aheavy chain CDR1 that is a CDR1 in SEQ ID NO: 142; a heavy chain CDR2that is a CDR2 in SEQ ID NO: 142; a heavy chain CDR3 that is a CDR3 inSEQ ID NO: 142; and a light chain polypeptide comprising the followingCDRs: a light chain CDR1 that is a CDR1 in SEQ ID NO: 144; a light chainCDR2 that a CDR2 in SEQ ID NO: 144; and a light chain CDR3 that is aCDR3 in SEQ ID NO: 144; or (b) a heavy chain polypeptide comprising thefollowing complementarity determining regions (CDRs): a heavy chain CDR1that is a CDR1 in SEQ ID NO: 2; a heavy chain CDR2 that is a CDR2 in SEQID NO: 2; a heavy chain CDR3 that is a CDR3 in SEQ ID NO: 2; and a lightchain polypeptide comprising the following CDRs: a light chain CDR1 thatis a CDR1 in SEQ ID NO: 19; a light chain CDR2 that a CDR2 in SEQ ID NO:19; and a light chain CDR3 that is a CDR3 in SEQ ID NO: 19; and alabeled second antibody that is anti-immunoglobulin; binding the firstmonoclonal antibody to an EGFRvIII antigen in patient tissues or cells;detecting a reaction of the first monoclonal antibody with the EGFRvIIIantigen, thereby screening the patient tissues or cells for epithelialcancer; and selecting the patient as having the epithelial cancer.